a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm,
genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots
methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet,
varSelRF
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 3.6), adductData, ExperimentHub, AnnotationHub
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
R (>= 3.2.0), grid, GenomicRanges (>= 1.31.8),
SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6)
R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings,
hypergraph
R (>= 3.6), impute, doParallel, grDevices, dplyr, methods,
ComplexHeatmap
R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData
R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db
R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges
BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges
(>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy,
lumi
R (>= 3.6.0), SummarizedExperiment, ROCR
methods, grDevices, stats, utils, parallel, edgeR
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.4), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
R (>= 2.3.0), methods, GenomicRanges, abind, parallel
R (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase
R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr
R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 3.6.0), methods, utils, graphics, stats, parallel
R (>= 3.5.0), reticulate, methods, SummarizedExperiment, knitr
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 3.5), shiny, igraph, shinyBS, pathview
limma, MASS, R(>= 2.10), Biobase, methods
R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24),
GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula
ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel,
Biobase
R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.6), GenomicRanges, cowplot, breakpointRdata
R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.29.14),
SummarizedExperiment (>= 1.9.18)
R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23),
GenomeInfoDb, GenomicRanges, foreach, iterators, methods,
parallel, locfit
R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio
R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>=
1.38.2), SummarizedExperiment (>= 1.8.1)
methods, MultiAssayExperiment, R (>= 3.5.0)
R (>= 2.14.0), Biobase, binom, methods, stats
BiocGenerics, BiocParallel, EBImage, graphics, methods,
S4Vectors (>= 0.23.18), stats, ProtGenerics
R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 3.6), SingleCellExperiment, magrittr, methods, stats,
tibble, utils
R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz,
XML, ggplot2
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.3), minfi, ChAMPdata (>= 2.6.0), FEM (>= 3.1),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest,
DT
R (>= 3.6), ggplot2, SingleCellExperiment
Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1),
GenomicAlignments, methods, AnnotationDbi,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens
Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors,
ensembldb, AnnotationFilter, data.table
R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll,
parallel
R (>= 3.2), methods, grid, IRanges (>= 2.13.12), Biostrings
(>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25),
VennDiagram
R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19)
R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS,
graphics, stats, changepoint
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
R (>= 3.3), GenomicRanges, ggplot2, chromstaRData
R (>= 3.5.0), methods, S4Vectors (>= 0.18.0),
MultiAssayExperiment (>= 1.6.0), BiocParallel
R (>= 2.15), BiocGenerics (>= 0.1.0), methods, stats
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment,
BiocGenerics
R (>= 3.4), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
R (>= 2.12), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.10), methods, tools, stats, genefilter
brglm, doParallel, foreach, GenomicRanges, methods,
splitstackshape
R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags,
ggplot2, gridExtra
R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
2.17.8), limma
R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
R (>= 3.6.0), grid, utils, biomaRt, Gviz, psych
R (>= 3.5.0), minfi, Homo.sapiens, mixOmics
R (>= 3.1.1), methods, topGO, GenomicRanges
R (>= 3.1.2), methods, grid, graphics, stats, grDevices
R (>= 2.10), BiocGenerics, IRanges, GenomicRanges,
BiocParallel
R (>= 3.0), minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylationEPICmanifest
R (>= 2.14), igraph, shiny, arules, methods
R (>= 3.4.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 3.3.0), shiny, shinyjs, CRISPRseek
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1)
R (>= 3.0.1), methods, biomaRt, grImport2, grid, motifStack
R (>= 3.4), SummarizedExperiment, ggplot2
R (>= 3.6.1), foreach, parallel, doParallel, igraph
R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1),
stats, parallel
R (>= 3.5.0), AnnotationDbi, BiocParallel,
SummarizedExperiment, limma
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.13.44),
R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>=
0.31.5), S4Vectors (>= 0.24.4), IRanges (>= 2.17.3),
BiocParallel
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment,
knitr, KernSmooth, matrixcalc
BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice
S4Vectors (>= 0.23.18), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R(>= 3.6.0), R.utils, DESeq2, BiocParallel
BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11),
AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18)
R (>= 3.5), GenomicRanges, SummarizedExperiment
R (>= 3.5), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 3.6.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges
R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10)
R (>= 3.6.0), minfi, SummarizedExperiment
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
R (>= 3.3), Biobase, bsseq, splines, methods
blockmodeling, gplots, testthat, R (>= 3.0.0)
isa2, Biobase (>= 2.17.8), AnnotationDbi, methods
R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 1.99.0),
GenomicRanges
BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18),
GenomicFeatures (>= 1.29.10), AnnotationFilter (>= 1.5.2)
R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2,
foreach, Rtsne, igraph
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2)
R (>= 3.5), Rsamtools, GenomicRanges, ShortRead
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment,
cluster (>= 2.0.7-1), fpc (>= 2.2-3)
R (>= 3.4), SGSeq, Matrix, SummarizedExperiment
Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.17.9),
BiocFileCache (>= 1.5.1)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.13.11)
R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2
caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db,
AnnotationDbi
methods, LiquidAssociation, parallel, doParallel, stats,
Hmisc, utils
R (>= 3.3.0), S4Vectors, IRanges, GenomicRanges, grid
R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram
R (>= 2.15.0), methods, Biobase, rrcov, flowCore
R (>= 2.11.0), flowCore, flowViz,flowClust
R (>= 3.2), methods, flowCore, flowViz, flowStats
R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11),
splines, methods, LSD
R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene,
FunciSNP.data
R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>=
0.5.32)
R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0),
methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10)
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0),
Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3)
R (>= 3.6), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt,
ggplot2
R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics
(>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs
R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>=
1.17.19), SummarizedExperiment (>= 1.1.6)
R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel,
Homo.sapiens
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
R (>= 3.5), Matrix, MultiAssayExperiment, glmnet
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome,
data.table
R (>= 3.5.0), grid, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg38.knownGene,
R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges
(>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7)
R (>= 3.2), penalized, Iso, survival, methods,
graph,stats,glmnet,mvtnorm
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 3.2.0), GenomicRanges, BiocGenerics
GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges,
magrittr, ggplot2, methods, stats,utils ,knitr,dplyr
methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>=
2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3),
BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>=
1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer
(>= 1.33.8), GenomeInfoDb, SummarizedExperiment
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
R (>= 3.6), utils, curl, rhdf5, R6, grid
R (>= 3.6), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R
(>= 3.0)
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer,graphics,GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
methods, R (>= 3.6.0), Rcpp (>= 0.12.0), SummarizedExperiment,
StanHeaders (> 2.18.1)
R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>=
2.7.20)
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R(>= 3.6), methods, stats, graphics, grid, lattice, grDevices,
flowCore
graphics, grDevices, stats, utils, parallel, compiler, R (>=
3.2.3)
R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures,
S4Vectors
R (>= 3.5), methods, Biobase, BiocParallel
R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
MultiAssayExperiment, SummarizedExperiment,stats
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 2.10), methods, BiocGenerics, grid
R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment,
edgeR, S4Vectors
R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats,
utils
R (>= 2.12.0), MASS, Matrix, XML, digest, bitops
R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3),
S4Vectors (>= 0.23.22)
R (>= 3.5), DiscriMiner, SummarizedExperiment
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.2.2), methods, SummarizedExperiment (>= 0.2.0), Rcpp
(>= 0.11.0), RcppArmadillo (>= 0.3.4.4)
R (>= 3.4), regioneR, GenomicRanges, methods
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy
R (>= 3.5.0), S4Vectors, SingleCellExperiment,
SummarizedExperiment, methods, rhdf5, rtracklayer
R (>= 2.10), convert, graph, limma, marray, methods
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
R (>= 3.5), BiocParallel, methods, stats, biglm
RUnit, BiocGenerics, BiocParallel, GenomicRanges,
SummarizedExperiment
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
lattice, MASS, proto, foreign, gWidgets(>= 0.0-36),
gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca
R (>= 2.15), grDevices, graphics, methods, stats, utils
R (>= 2.10.0), survival, Biobase, MASS, methods
R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 2.13.0), EDASeq, DESeq, limma, qvalue
R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table,
Biobase, digest
R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings
R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn,
grid,sqldf
R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb,
GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db
R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods
R (>= 3.2.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2
R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats,
cluster, marray, mclust, RColorBrewer, colorspace, igraph,
Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
methods, BiocGenerics (>= 0.15.3), GenomicRanges,
SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>=
1.1.9)
R (>= 3.2), Biobase (>= 2.22.0), miRcompData
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata,
KernSmooth
R (>= 3.5), methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools
R (>= 2.13.0), methods, Biobase, xtable, limma, statmod,
lattice, vsn
R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges,
Biostrings
R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel,
methods, grid, graphics, BSgenome, XVector,
BSgenome.Hsapiens.UCSC.hg19
R (>= 2.15.1), methods, grImport2, grid, MotIV, ade4,
Biostrings
R (>= 2.10), graphics, BiocGenerics, GenomicRanges
R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
limma
viridis, S4Vectors, GenomeInfoDb, GenomicAlignments,
VariantAnnotation
R (>= 3.6.0), SummarizedExperiment (>= 1.3.81)
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors,
SummarizedExperiment
R (>= 3.6), SummarizedExperiment, S4Vectors
R (>= 2.14.0), flowCore(>= 1.51.7), RcppArmadillo, methods, BH
R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2
R (>= 3.6.0), BiocGenerics, ggplot2, tibble (>= 1.3.1)
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10),
AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.23.31)
R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
R (>= 3.6), BiocParallel, GenomicFeatures,
SummarizedExperiment, data.table, methods
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.4), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.3.0), methods, ggplot2, gridExtra
R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz
ggplot2, ggrepel, reshape2, lattice, grDevices, cowplot
R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats,
ppiData, annotate (>= 1.17.4)
R (>= 3.5.0), IRanges, GenomicRanges, Biostrings (>= 2.26.3),
data.table, rTANDEM
R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods,
Biobase (>= 2.5.5)
R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2
R(>= 2.15.0), chipseq, IRanges, GenomicRanges
R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1),
BiocGenerics, S4Vectors
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges
(>= 1.28.4)
R (>= 3.2.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph,
graph, graphite
biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb,
yeastExpData
R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov
R (>= 2.14.0), GenomicAlignments, affy, RPA
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 3.6), BiocGenerics, SummarizedExperiment
R (>= 3.2.2), methods, IRanges, biomaRt (>= 2.34.1),
BiocGenerics, httr, plyr
R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1)
reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
testthat
R (>= 3.5), Biostrings, BiocGenerics,methods
R (>= 3.6), parallel, GenomicRanges (>= 1.13.3), Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11),
Biostrings (>= 2.47.6), Biobase
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.0.2), GenomicRanges, VariantAnnotation
R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq
R (>= 3.2), Biobase, rcdk, fingerprint, rcellminerData
R (>= 2.14.1), methods, graph, GOstats, ggplot2
R (>= 2.13.0), GenomicRanges, GenomicAlignments, ggplot2,
ComplexHeatmap
R (>= 2.15.0), BiocGenerics (>= 0.1.0),
BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome,
ChIPpeakAnno
R (>= 2.15.0), methods, IRanges, PSICQUIC, AnnotationHub,
RCurl, shiny
R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0)
Rsamtools, GenomicRanges, IRanges, data.table, methods,
parallel
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.1.2), GenomicRanges, IRanges, methods
R (>= 3.0.2), methods, GenomicRanges, abind
methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges,
GenomicRanges, SummarizedExperiment, Rsamtools,
GenomicAlignments, rtracklayer
R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice
R (>= 3.6), IRanges (>= 2.19.7), S4Vectors (>= 0.23.18),
GenomicRanges, Modstrings
R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments
R(>= 3.5.0), ggplot2, pathview, edgeR, methods
R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2),
gplots, gridExtra, limma, matrixStats, methods, illuminaio,
methylumi, plyr
R (>= 3.6.0), Biobase, ggplot2, limma, methods
R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt,
Biostrings, Biobase, DBI
methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz
R (>= 3.1.1), affy, BiocGenerics, methods
methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase,
RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2),
AnnotationDbi
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),
Biostrings (>= 2.47.6)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
R (>= 3.3), methods, GenomicRanges (>= 1.37.2)
R (>= 3.4.0), biclust, SummarizedExperiment
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.31.1)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 3.6), SummarizedExperiment, dynamicTreeCut,
SingleCellExperiment
SingleCellExperiment (>= 1.7.4), Seurat, ggplot2
R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.4), ggplot2, methods, SingleCellExperiment
R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings,
IRanges, plyr, tcltk
R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
2.15.0), methods
R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>=
1.20.3)
R (>= 3.5.0), IRanges (>= 2.13.15), GenomicRanges (>=
1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods
methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>=
1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R
(>= 3.0.0)
rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma
R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost,
BiocGenerics
R (>= 3.5), SummarizedExperiment, SingleCellExperiment,
DelayedArray, Biobase
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 3.1), GenomicRanges, Rsamtools, data.table, checkmate
R (>= 3.2.0), BiocGenerics, SummarizedExperiment
R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF
R (>= 3.6), Seurat, SingleCellExperiment,
SummarizedExperiment, dplyr
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
Rgraphviz (>= 2.3.7)
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 3.5.0),SummarizedExperiment, methods, Rcpp, shiny
R (>= 3.3.1), EBcoexpress, MASS, igraph, pvclust (>= 2.0-0),
gbm (>= 2.1.1), limma, DMwR (>= 0.4.1), matrixStats, Hmisc
R (>= 2.12), methods, qvalue, lattice, limma
R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
R (>= 3.6), S4Vectors (>= 0.23.18), IRanges, Biostrings
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 3.6.0)
R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors,
BiocGenerics, methods, UpSetR, rlang, stringr, utils,
BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo,
crayon, tibble
R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase,
DelayedArray (>= 0.3.20)
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2),
ggplot2, plyr, openxlsx
R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC
R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6.0), e1071, quadprog, SummarizedExperiment
R (>= 3.3.0), methods, utils, ProtGenerics
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.1.0), grDevices, methods, GenomicRanges, grid
R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18)
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite
R (>= 2.15.2), methods, BiocGenerics, Biobase
methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8)
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
R (>= 3.5.0), ggplot2, limma, foreach, scales, Biobase,
methods
R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb
(>= 1.15.2), GenomicRanges (>= 1.37.4), SummarizedExperiment
(>= 1.9.9), Rsamtools (>= 1.99.0)
R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>=
1.13.0), GenomicRanges, GDSArray (>= 1.3.0), DelayedDataFrame
(>= 1.0.0)
R (>= 3.0.0), methods, BiocGenerics (>= 0.25.1),
VariantAnnotation (>= 1.13.29)
S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges
(>= 1.31.8), VariantAnnotation (>= 1.11.16), methods
R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)
R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel,
foreach
R (>= 3.4), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene,
zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools
oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 2.14.0), methods, Biobase, BiocParallel (>= 1.8.0),
MSnbase (>= 2.9.3)
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.3.0), GenomicRanges, ggplot2, grid
R (>= 3.4), methods, SummarizedExperiment,
SingleCellExperiment
Biobase, graphics, grDevices, methods, multtest, stats, tcltk,
utils
ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr,
flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra,
rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly,
BiocStyle, stringr, utils, methods, grDevices, stats, tools,
graphics
Biobase, QDNAseq, ggplot2, grid, stats, utils, methods,
grDevices, GenomicRanges
Biobase, cluster, grDevices, graphics, methods, multtest,
stats, survival, splines, utils
bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH,
snapCGH
methods, graphics, stats, utils, calibrate, origami (>=
1.0.0), SummarizedExperiment, S4Vectors, tmle
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods,
multtest (>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils, zlibbioc
affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, BiocManager,
R2HTML, xtable
affy, affyPLM, Biobase, genefilter, graphics, grDevices,
lattice, RColorBrewer, simpleaffy, stats, utils, xtable
BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest
rmarkdown, tools, methods, ggplot2, GGally, dplyr, rjson,
shiny, shinydashboard, DT, stats, utils, tximport (>= 1.11.5),
cowplot
methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3),
VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6),
S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>=
1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice,
latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme
Biostrings, IRanges, GenomicRanges, GenomicAlignments,
Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm,
splines, graph, RBGL, stringr, stats, methods, graphics,
GenomeInfoDb, S4Vectors
assertthat, BiocParallel, ChIPseeker, corrplot, data.table,
dplyr, GenomicRanges, GGally, genefilter, gghalves, ggplot2,
ggseqlogo, Gviz, magrittr, org.Hs.eg.db, plyr, reshape2,
rtracklayer, stats, stringr, tibble, tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, utils
callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
MultiAssayExperiment, circlize, curatedTCGAData, foreach,
glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2,
gridExtra, utils
methods, log4r, tools, rjson, Biobase, graph
stats, DBI, limma, lumi, agricolae, RMySQL, DESeq2,
SummarizedExperiment, gplots, gage, S4Vectors
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb,
IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings,
GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster,
mclust
igraph, Biobase, survival, MASS, stats, RColorBrewer
assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2,
rentrez, reshape2, covr, ape, vegan, dplyr, magrittr,
MultiAssayExperiment, SummarizedExperiment, S4Vectors (>=
0.23.19), XML, forcats, scales, lattice, glmnet, tsne, DMwR,
plotROC, DT, reactable, utils, limma, methods, stats, tibble,
biomformat, umap, Matrix
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), RCurl
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors,
interactiveDisplayBase, httr, yaml, dplyr
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocManager, biocViews, AnnotationDbi, Biobase,
Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi,
RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>=
1.3.0), XML, RCurl
AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures,
GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges,
methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>=
0.23.10), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq,
SummarizedExperiment, Rsubread, stats, methods
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
shiny, shinyjs, DT, VariantAnnotation, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings,
MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5,
MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.1.hs37d5,
COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131,
SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr,
utils, stats, GenomicRanges, S4Vectors, GenomicFeatures,
IRanges, GenomicScores, SummarizedExperiment
Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges,
Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools,
ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods,
rJava, stats, svMisc, utils, sendmailR, bitops
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter,
graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter,
lattice, latticeExtra, limma, methods, RColorBrewer, setRNG,
stats, utils, vsn (>= 3.23.3), XML, svglite
affy, Biobase, graphics, grDevices, limma, methods, stats,
utils, xtable
methods, foreach, S4Vectors (>= 0.9.25), IRanges (>= 2.13.24),
DNAcopy, oligoClasses (>= 1.21.3)
AnnotationDbi, biomaRt, bit64, circlize, cluster,
ComplexHeatmap, corrplot, data.table, dplyr, factoextra,
FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel,
gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx,
org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap,
plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr,
tidyr, UpSetR, utils, VennDiagram, yaml
BiocParallel, ggplot2, grDevices, gridExtra, methods, PepsNMR,
plyr, quadprog, ropls, stats, SummarizedExperiment, TSdist,
utils, Matrix, zoo
BiocParallel, GenomicAlignments, GenomicFeatures,
GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma,
S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr,
fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer,
scales, grid, ggplot2, mGSZ, utils
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools,
BiocStyle
Biostrings, GenomicRanges, IRanges, graphics, grDevices,
methods, stats, utils
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats,
motifStack, preseqR, utils, KernSmooth, edgeR
BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table,
ggplot2, grDevices, graphics, grid, motifStack, rappdirs,
stats, testit, utils
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
data.table, graphics, grDevices, GSEABase, methods, mixtools,
R.utils, shiny, stats, SummarizedExperiment, BiocGenerics,
S4Vectors, utils
MSnbase, devtools, RColorBrewer, dplyr, rlang, plyr, mzR,
assertthat, scales, methods, entropy, cluster, grDevices,
graphics, stats, utils
GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
reshape2, scales, coda, foreach, ggplot2, methods, utils,
graphics, stats
VariantAnnotation, Rsamtools, biomaRt, GenomicRanges,
S4Vectors, utils, stats, grDevices, graphics
GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors
(>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>=
1.29.25), Biobase (>= 2.25.0), GenomeInfoDb
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
Biobase, BiocGenerics, coda, cowplot, data.table, ggExtra,
ggplot2, graphics, grDevices, KernSmooth, MASS, matrixStats,
methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4,
SummarizedExperiment, viridis, utils, Matrix
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, scater, BiocParallel
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, d3heatmap, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
parallel, MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices,
GenomicRanges, IRanges, Biostrings
Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
ggplot2, SingleCellExperiment, data.table, stats, utils,
graphics, compiler
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
outliers, abind, stats, graphics, utils, methods
data.table, RCurl, digest, methods, stats, utils, dplyr,
graph, Biobase
stats, utils, GEOquery, graphics, BiocGenerics
shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0),
methods, shinythemes, Biobase, geNetClassifier,
AnnotationFuncs, org.Hs.eg.db, DOSE, clusterProfiler,
reactome.db, ReactomePA, DiagrammeR(>= 1.0.5), visNetwork,
htmlwidgets, plyr, tibble, DT (>= 0.12), dplyr (>= 0.8.5)
biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr,
tools, optparse, codetools, methods, utils, knitr
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl,
httr
methods, utils, graphics, stats, parallel
Rgraphviz, geneplotter, graph, BiocGenerics, methods
Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr,
rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges,
IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures,
curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
stats, utils, futile.logger, parallel, snow
BiocFileCache, BiocManager, biocViews, tibble, methods, rlang,
tidyselect, stringr, rvest, rex, dplyr, xml2, rappdirs, readr,
httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh,
RBGL, graph, magrittr
methods, tibble, utils, rlang, plyr, rtracklayer,
AnnotationDbi, KEGGREST
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, irlba, rsvd, Rcpp
bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
utils, XML, AnnotationDbi, progress, stringr, httr, openssl,
BiocFileCache, rappdirs
stats, utils, grDevices, lattice, BiocParallel, glmnet, rms,
nsprcomp, ranger, e1071, variancePartition, ggplot2, pROC,
vioplot, CMplot
igraph (>= 1.0.1), AnnotationDbi, Biobase
BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr,
utils, stats, RColorBrewer, Hmisc, psych, knitr
Biostrings, ipred, e1071, klaR, randomForest, class, tree,
nnet, rpart, party, foreign, Biobase, utils, stats, grDevices
BiocGenerics, Biobase, methods, grid, graphics, NMF
igraph, cluster, psych, stringr, GenomicRanges
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, future, doFuture, tmle (>= 1.4.0.1), S4Vectors,
BiocGenerics, BiocParallel, SummarizedExperiment, limma
grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28),
GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),
SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=
1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=
1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),
ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang
readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools,
data.table, Biobase, GenomicRanges, BiocGenerics,
VariantAnnotation, DelayedMatrixStats, SummarizedExperiment,
GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats,
rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer,
parallel, betareg, lokern, Formula, globaltest
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8),
BiocGenerics, grDevices, stats, graphics
Rcpp (>= 0.12.12), IRanges, GenomeInfoDb, S4Vectors,
matrixStats, preprocessCore, sva, parallel, EBImage, utils
assertthat, methods, MASS, doParallel, parallel, e1071, earth,
foreach, randomForest, stats, IRanges, S4Vectors, data.table,
graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc,
magrittr, kernlab, ggplot2, cowplot, BiocStyle
Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder
(>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>=
1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils,
grDevices, GenomicState (>= 0.99.7)
plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt,
Biostrings, parallel, utils, stats,
BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges,
GenomeInfoDb, IRanges, S4Vectors, data.table
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, curl, xml2, grDevices, rlang,
BiocFileCache, rappdirs
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
rtracklayer
IRanges (>= 2.11.16), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>=
0.23.11), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2),
permute, limma, DelayedArray (>= 0.9.8), Rcpp, BiocParallel,
BSgenome, Biostrings, utils, HDF5Array (>= 1.11.9), rhdf5
BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2,
WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra,
biovizBase, e1071, methods, grDevices, stats, utils
devtools, stringi, gtools, stats, utils, SummarizedExperiment,
Biostrings, IRanges
matrixStats, limma, doRNG, BiocGenerics, utils,
GenomicFeatures, AnnotationDbi, stats
gplots, methods, grDevices, stats, SummarizedExperiment
AnnotationDbi, AnnotationFilter, biomaRt, Biostrings,
BSgenome, data.table, dplyr, ensembldb, GenomeInfoDb,
GenomicFeatures, GenomicRanges, magrittr, Matrix, methods,
plyranges, Rcpp, RcppParallel, S4Vectors, stats, stringr,
tibble, tidyr, zeallot
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
beanplot, BiocGenerics, BiocParallel, BSgenome, data.table,
DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments,
GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges
(>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape,
rtracklayer, S4Vectors, som, stringdist, stringi,
SummarizedExperiment, utils, vegan, VGAM
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR,
pcaPP, apcluster, graphics
GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart,
survival, Biobase, phenoTest, circlize, plyr, graphics, stats,
utils, grDevices
SNFtool, iCluster, cluster, impute, limma,
ConsensusClusterPlus, grDevices, survival
Biobase, dplyr, irlba, lattice, Matrix, matter, magrittr,
mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite
BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools,
rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM
Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus,
cowplot, data.table, dplyr, drc, DT, flowCore, FlowSOM,
ggplot2, ggrepel, ggridges, graphics, grDevices, grid,
gridExtra, htmltools, limma, magrittr, Matrix, matrixStats,
methods, nnls, plotly, purrr, RColorBrewer, reshape2, Rtsne,
SingleCellExperiment, SummarizedExperiment, S4Vectors, scales,
scater, shiny, shinydashboard, shinyBS, shinyjs, stats, utils
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots,
grDevices, stats, utils, xlsx
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack
(>= 0.7)
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
stats, plyr, foreach, ggplot2, RColorBrewer, grid, scales,
gtable, grDevices, graphics, matrixStats, doParallel, digest,
gridExtra, methods, reshape2, MAST, S4Vectors, data.table,
Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
pROC, magrittr
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise,
purrr (>= 0.3.0), rappdirs, tidyr, lubridate
prada, GSEABase, Category, stats4, BiocGenerics
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
BiocNeighbors, ggplot2, scater, viridis, cowplot,
SummarizedExperiment, SingleCellExperiment, tidyr, magrittr,
dplyr, ggridges, stats, purrr, listarrays, methods,
BiocParallel, BiocGenerics
BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
topicmodels, slam, maptpx, igraph, xtable, gplots
methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid,
ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler,
fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools,
pracma, intergraph, grDevices, utils, network, matrixStats,
ggdendro, gridExtra, gtable
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,kpmt,ggplot2,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
SummarizedExperiment, FactoMineR, factoextra, IRanges,
graphics, modes, parallel, plyr, cluster, diptest, stats,
matrixStats
BiocGenerics, zlibbioc, Rcpp (>= 0.11.0)
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg
gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
ChIC.data (>= 1.3.3), caTools, methods,GenomicRanges, IRanges,
parallel, progress, caret, grDevices, stats, utils, graphics,
S4Vectors, BiocGenerics
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments,
RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db,
org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr,
BiocStyle, ArgumentCheck, gtools, magick
AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb,
GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra,
MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer,
S4Vectors (>= 0.23.10), stats, stringr, utils
methods, utils, GenomeInfoDb, stats, BiocParallel,
GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>=
1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>=
0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>=
1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3),
hexbin (>= 1.27), rmarkdown
BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome,
GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi,
limma, multtest, RBGL, graph, BiocManager, stats, regioneR,
DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments,
DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools
BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>=
1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>=
1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods,
reshape2, Nozzle.R1, Biobase, grDevices, stats, utils,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Celegans.UCSC.ce6.ensGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene
AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges,
GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots,
graphics, grDevices, gtools, methods, plotrix, dplyr, parallel,
magrittr, RColorBrewer, rtracklayer, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene, utils
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots,
ggplot2, LSD, corrplot, methods, stats, grDevices, graphics,
utils, BiocGenerics, S4Vectors
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
graphics, stats, utils, methods, survival
cluster, DPpackage, ICSNP, ellipse, vegan
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb,
IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals,
mvtnorm
IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor,
BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools,
S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats,
utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment,
RColorBrewer, BSgenome
XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx,
igraph, circlize, graph, stats, utils, grDevices, graphics,
methods, biomaRt
bitops,gplots,grDevices,som,
dplyr,gridExtra,png,stringr,S4Vectors, IRanges,
GenomeInfoDb,graphics, stats, utils
dplyr, magrittr, readr, rtracklayer, stringr, Biostrings,
BSgenome, stringi, DESeq2, edgeR, GenomicRanges, IRanges,
seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors,
stats, AnnotationHub, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges,
utils, BSgenome.Drerio.UCSC.danRer7
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix,
matrixStats, methods
mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally,
ggplot2, plotly, methods, utils, stats, sna, grDevices,
graphics, Biobase, gplots, MSnbase
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, howmany, locfdr, matrixStats, graphics, parallel,
RSpectra, kernlab, stringr, S4Vectors, grDevices, DelayedArray
(>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR,
scales, zinbwave, phylobase, pracma
AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7),
ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue,
rvcheck, stats, tidyr, utils
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors, exomeCopy
IRanges, GenomicRanges, SummarizedExperiment, pracma,
regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics,
utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings,
methods
S4Vectors, grDevices, stats, utils, NOISeq, IRanges,
Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb,
gplots, reshape2, stringr, testthat, graphics, methods, shiny,
shinyFiles, shinyjs, grid, openxlsx
BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors,
SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt,
grDevices, lattice, limma, methods, plyr, qqman, rappdirs,
reshape2, stats, utils
methods, seqinr, yaml, rtfbs, gplots, mclust, gmp,
BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome,
biomaRt
BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
grDevices, simpleCache, fitdistrplus
affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma,
graphics, stats, utils, STRINGdb, SummarizedExperiment, minet,
rmarkdown
BiocParallel, cluster, methods, gplots, graphics, grDevices,
RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tools, utils, rhdf5
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, dplyr, devtools
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.0.0), matrixStats, GetoptLong, circlize (>= 0.4.7),
GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
cluster, skmeans, png, mclust, crayon, methods, xml2,
microbenchmark, httr, knitr, markdown, digest, impute, brew,
Rcpp (>= 0.11.0), BiocGenerics, eulerr
colortools, hash,grDevices, gridExtra, rtracklayer, IRanges,
S4Vectors, GenomicRanges, stats, corrplot
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown
tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16),
gplots, gtools, gdata, caTools, grid, KernSmooth, MASS,
ggplot2, stringr, modeest, edgeR, limma, vioplot, methods
AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel,
grDevices, gplots, IRanges, GenomicFeatures, XVector,
methylPipe, GO.db, S4Vectors, GenomeInfoDb
rtracklayer, Rgraphviz, ggplot2, GenomicFeatures,
TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2,
pathview
circlize (>= 0.4.5), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png
matrixStats, gplots, grDevices, methods, graphics, stats,
utils
Biobase, ALL, graphics, stats, utils, cluster
airway, AnnotationDbi, BiocParallel, Biobase, Biostrings,
data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb,
edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures,
limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools,
RUVSeq, S4Vectors, stats, SummarizedExperiment,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils
Biobase, GSVA, gdata, genefu, limma, matrixStats,
randomForest, stats, utils, methods
GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
data.table, grDevices, clue, cluster, gplots, BiocGenerics (>=
0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP,
GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy,
colorspace, reshape2, ggplot2, methods, exomeCopy,
GenomicAlignments, diagram
methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
GenomeInfoDb
regioneR, IRanges, Rsamtools, SummarizedExperiment,
VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges,
cn.mops, rhdf5, utils
matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges,
Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges,
CopyhelpeR, GenomeInfoDb, futile.logger
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2
(>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8),
grDevices, graphics, stats, methods, compositions, mvtnorm
SQUAREM, slam, maptpx, plyr(>= 1.7.1), cowplot, gtools,
flexmix, picante, limma, parallel, reshape2, stats, utils,
graphics, grDevices
rmarkdown (>= 0.9.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods
S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
parallel, genefilter, grDevices, stats, graphics
methods, corpcor, BiocParallel, ggplot2, plyr
parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
BSgenome, BiocParallel, hash
DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures,
BiocManager, BSgenome, AnnotationDbi, hash
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
matrixStats, VGAM, parallel, graphics, limma, beanplot
data.table, methods, MergeMaid, ConsensusClusterPlus, limma,
cluster, dplyr, Biobase, grDevices, stats, graphics, utils
Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures,
AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb,
stats, BiocParallel, utils
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache, rappdirs
biomaRt, cowplot, data.table, dplyr, fgsea, ggplot2, ggrepel,
graphics, httr, limma, methods, pbapply, R.utils, readxl,
reshape2, rhdf5, stats, tools, utils
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges,
Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>=
2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr,
VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite,
AhoCorasickTrie, methods
shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite,
ape, WGCNA, RTCGAToolbox
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp,
BiocNeighbors, SummarizedExperiment
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats,
grDevices, Rdpack, methods, grid, FlowSOM
flowCore (>= 1.43.10), flowWorkspace (>= 3.33.10), openCyto
(>= 1.11.3), XML, data.table, jsonlite, RBGL, ncdfFlow,
Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc,
plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml,
lattice, stats, corpcor, RUnit
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils
DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap,
FactoMineR, corrplot, randomForest, e1071, caret, MASS,
lubridate, plsVarSel, kknn, FSelector, methods, stats, utils,
graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR
MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png,
lattice,reshape2,gplots,pcaMethods,ggplot2,
limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics,
openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot,
imp4p (>= 0.8), highcharter (>= 0.7.0), DAPARdata (>= 1.16.0),
siggenes, graph, lme4, readxl, clusterProfiler, dplyr,
tidyr,AnnotationDbi, vsn, FactoMineR, factoextra, visNetwork
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
methods, stats, utils, ggplot2, fdrtool, reshape2,
GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr,
assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT,
ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE,
igraph, grDevices, graphics, stats, utils, GenomicRanges,
IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2,
d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR,
clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker,
plotly, heatmaply, Harman, pathview
methods, DBI, S4Vectors, IRanges, XVector
stats, methods, ggplot2, foreign, graphics, BiocStyle,
Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4,
sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2,
gridExtra
Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment,
ComplexHeatmap, grid, parallel, BiocParallel, grDevices,
graphics, stats, methods, utils
methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges,
stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors,
plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
SummarizedExperiment, ggseqlogo, gridExtra, data.table
GenomicRanges, data.table, stringr, diffr, dplyr, methods,
rjson, utils, R.utils, foreach, withr, rtracklayer,
GenomeInfoDb, settings, filehash
checkmate, data.table, DESeq2, edgeR (>= 3.13.4),
GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment
utils, methods, Biobase, BiocGenerics, broom, circlize,
ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2,
dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices,
knitr, logging, lasso2, magrittr, Nozzle.R1, psych,
RColorBrewer, reshape, rlang, scales, stats, stringr,
S4Vectors, SummarizedExperiment, tidyr, tibble
graphics, grDevices, methods, stats, utils
methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>=
0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2
matrixStats, stats, truncdist, base64enc, ggplot2
ggplot2, dplyr, purrr, readr, tibble, tidyr,
SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool,
ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny,
shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid,
stats, imputeLCMD, cluster
BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9),
BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2),
derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges
(>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>=
1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>=
0.23.19), stats
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>=
1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28),
limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>=
0.9.38), scales, utils
BiocParallel, BiocGenerics, ChIPpeakAnno, data.table,
DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges,
plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19),
SummarizedExperiment, tools, utils
genefilter, geneplotter, methods, MASS, RColorBrewer
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, stats4, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>=
0.11.0)
methods, graphics, grDevices, utils, stats, Matrix, Rcpp (>=
0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods,
Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2,
Matrix, jsonlite, tools, DESeq2, methods
BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb,
GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats,
utils
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
RColorBrewer, amap, edgeR, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, lattice,
systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel,
parallel, S4Vectors, Rsamtools (>= 1.99.1), DESeq2, methods,
graphics, ggrepel
stats, DiffCorr, psych, igraph, BiocGenerics
flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma,
edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats,
methods, utils, grDevices, graphics, ComplexHeatmap, circlize,
grid
graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils
Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma,
csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb,
BiocGenerics, grDevices, graphics, stats, utils, Rcpp,
rtracklayer
methods, GenomicRanges, foreach, plyr, dplyr, reshape2,
ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt,
GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats,
utils, Biobase, readr, data.table, rtracklayer, pbapply, limma
grDevices, stats, methods, Matrix, MASS, expm, igraph, Rcpp,
RcppArmadillo, RcppParallel, plyr, precrec
Biobase, stats, biwt, gtools, MASS, tools
matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table,
ggplot2, ggExtra, dplyr, broom, shiny, shinyBS,
shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown,
knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply,
viridis, plotly, DT, gridExtra, methods, stats,
SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2
utils, stats, speedglm, MASS, data.table, splines, arm,
rtracklayer, benchmarkme, tibble, matrixStats, fastDummies,
graphics
utils, stats, grDevices, rtracklayer, multcomp, calibrate,
graphics
parallel, Rcpp, RcppRoll, betareg, grDevices, graphics,
methods, stats, utils
ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS,
missMethyl, GenomicRanges, methods, graphics, plyr, Gviz,
IRanges, stats, utils, S4Vectors
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb,
methods, mvtnorm, stats, parallel
GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer,
bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats,
BiocParallel, outliers, methods, locfit, IRanges, grDevices,
graphics, stats, utils, annotatr, AnnotationHub, rtracklayer,
GenomeInfoDb, splines
dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats,
utils, methods
biomaRt, data.table, utils, stats, Biostrings,
SummarizedExperiment, VariantAnnotation, AnnotationDbi,
GenomeInfoDb, IRanges, GenomicRanges, methods
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
d3heatmap, prodlim, matrixStats
AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
ggplot2, httr, dplyr, readr, stringr, tidyr
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
S4Vectors, BiocParallel, Rcpp, Matrix, methods, utils, stats,
edgeR, rhdf5, HDF5Array, R.utils, dqrng
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
stats, Rcpp (>= 0.11.3), ggplot2, reshape2, GO.db,
org.Hs.eg.db, AnnotationDbi, graphics
Biobase (>= 2.44.0), BiocFileCache (>= 1.7.10), BiocGenerics
(>= 0.30.0), BiocParallel (>= 1.18.1), biomaRt (>= 2.40.5),
Biostrings (>= 2.52.0), DESeq (>= 1.36.0), edgeR (>= 3.26.8),
GenomeInfoDb (>= 1.20.0), genomeIntervals (>= 1.40.0),
GenomicAlignments (>= 1.20.1), GenomicRanges (>= 1.36.1),
SummarizedExperiment (>= 1.14.1), graphics, IRanges (>=
2.18.3), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>=
0.3.1), Rsamtools (>= 2.0.3), S4Vectors (>= 0.22.1), ShortRead
(>= 1.42.0), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq,
aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings,
AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager
graphics, stats, utils, parallel, methods, ROCR, DESeq,
baySeq, snow, edgeR
methods, splines, sva, snm, jackstraw, qvalue(>= 1.99.0), MASS
graphics, stats, utils, methods, locfit, Rcpp
R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR,
DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db,
org.Mm.eg.db, limma, DOSE, AnnotationDbi
gplots, Biobase, GEOquery, limma, arrayQualityMetrics, impute,
RColorBrewer, zoo, igraph, plyr, Matrix, MASS, RCurl, affy
PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0),
limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5),
hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0),
safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap,
grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1),
Glimma (>= 1.4.0), htmlwidgets, plotly, DT
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, gespeR,RcppAnnoy (>= 0.0.9)
GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
methods, parallel, stats, utils, IRanges, GenomeInfoDb,
S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.9.2), plyr,
Matrix, dplyr, Gviz, ComplexHeatmap, circlize,
MultiAssayExperiment, SummarizedExperiment, biomaRt,
doParallel, downloader, ggrepel, lattice, magrittr, readr,
scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr,
tibble, tidyr, progress, purrr, ggpubr, rtracklayer,
DelayedArray
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
methods, tools, jsonlite, RCurl, tidyr, data.table, dplyr,
stringr, stringi, utils, AnnotationHub, GenomicRanges,
rtracklayer, S4Vectors, GenomeInfoDb
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap,
GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors,
SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma,
methods, pathview, rappdirs, safe, topGO
AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2,
ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices,
grid, gridExtra, igraph, methods, purrr, RColorBrewer,
reshape2, stats, utils
BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils,
methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr,
heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices,
magrittr
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>=
0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics,
Biostrings (>= 2.47.9), curl
S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment,
GenomeInfoDb, stats
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
data.table, doParallel, EntropyExplorer, graphics, stats,
grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA
BoolNet, e1071, gtools, stats, igraph, nem, utils, lattice,
latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph
epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4),
GenomicRanges, S4Vectors, IRanges
epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson,
methods, BiocGenerics
S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0),
OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb
git2r, epivizrServer, GenomeInfoDb, BiocGenerics,
GenomicFeatures, S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr
rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb,
Biobase, shiny, BiocParallel, IRanges, AnnotationDbi
Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
rJava, DiagrammeR, magrittr, digest, BSgenome, AnnotationDbi,
GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics,
S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid,
JASPAR2016, TFBSTools, grDevices, graphics, stats, utils,
parallel, corrplot, BiocManager, motifmatchr
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack
GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls,
limma, matrixStats, RBGL, prodlim, graph, methods, utils,
stats, doParallel, foreach, affxparser, GenomicRanges,
S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome,
BSgenome.Hsapiens.UCSC.hg38, Biostrings
stats, methods, grDevices, graphics, utils
utils, S4Vectors, BiocManager, curl, rappdirs
methods, ExperimentHub, BiocManager, DBI, BiocCheck, httr,
curl, biocViews, graph
methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi
methods, graphics, grDevices, stats, utils
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
affy, MASS, Biobase (>= 1.13.41), methods, graphics
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
methods, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>=
0.12.12)
methods, graphics, stats, BiocGenerics, S4Vectors, IRanges
ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment,
stats, mclust
fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap,
grDevices, stats, utils
FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph,
grid, intergraph, stringr, clusterProfiler, data.table,
grDevices, methods, network, scales, sna, utils, stats,
SingleCellExperiment, pathwayPCA
stats, plyr, VariantAnnotation, SummarizedExperiment,
rtracklayer, GenomicRanges, methods, IRanges
tcltk, graphics, grDevices, stats, utils
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2,
RColorBrewer, png
data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
gridExtra, grid, fastmatch, Matrix, utils
methods, BiocGenerics, Biobase, tools, dplyr, IRanges,
Biostrings, S4Vectors, kebabs, igraph, Matrix, digest,
filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro,
BiocParallel, utils, stats
graphics, stats, utils, methods, abind, gtools, qvalue,
S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
ggplot2, flowCore, plyr, changepoint, knitr, reshape2,
RColorBrewer, scales, methods, graphics, stats, utils,
rmarkdown
colorRamps, abind, BiocParallel, graphics, stats, utils,
plotly, shiny
methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid
BiocGenerics, methods, Biobase, graph, ellipse, flowViz,
flowCore, clue, corpcor, mnormt, parallel
Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats
flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos,
gplots, RFOC, flowWorkspace (>= 3.33.1), methods, stats,
grDevices
flowCore, flowViz, graphics, kza, methods, minpack.lm, gplots
Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices,
methods, stats, stats4
Biobase, graphics, grDevices, methods, rrcov, stats, feature,
flowCore
rrcov,flowCore, graphics, methods, stats, utils
flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny,
methods, graphics, stats, utils
stats, utils, flowCore, ConsensusClusterPlus, BiocGenerics,
tsne, flowWorkspace, CytoML, XML, RColorBrewer
FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase,
Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc,
RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster,
pheatmap, scatterpie, umap, scatterplot3d, limma, stringr,
grDevices, grid, stats
BiocGenerics, MASS, flowCore (>= 1.51.6), flowWorkspace,
ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods,
grDevices, graphics, stats, cluster, utils, KernSmooth,
lattice, ks, RColorBrewer, rrcov
flowCore, methods, flowViz, stats, flowClust
Biobase, graphics, grDevices, methods, flowCore, flowMeans,
sfsmisc, rrcov, flowClust, flowMerge, stats
Biobase, graph, methods, stats, utils, corpcor, RUnit, XML,
flowCore (>= 1.32.0)
stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
Biobase, BiocGenerics, graph, graphics, grDevices, lattice,
methods, stats, stats4, utils, RBGL, tools, gridExtra,
Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer,
stringr, scales, flowViz, matrixStats, digest, RcppParallel,
flowCore(>= 1.51.4), ncdfFlow(>= 2.31.1)
RUnit, methods, ChemmineR, BiocGenerics, parallel
DESeq2, Biobase, Biostrings, GenomicRanges,
SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer,
fda, GenomicAlignments, gtools, Matrix
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
shiny, fda, doParallel, GenomicAlignments, Rcpp, methods,
foreach, parallel, GenomeInfoDb, Rsamtools, grDevices,
graphics, stats, RColorBrewer
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1),
ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats,
ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges,
httr, IRanges, jsonlite, methods, VariantAnnotation
AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
stats, utils, methods, Matrix, fastmatch, plyr, dplyr,
magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db,
org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase,
BiocFileCache, matrixStats
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9),
parallel, annotate, genefilter, AnnotationDbi, DESeq,
grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras
(>= 1.1.2)
brew, BiocGenerics, annotate, AnnotationDbi, graphics,
grDevices, GSEABase, hwriter, parallel, stats, utils, yaml
Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db,
rmarkdown, grDevices, graphics, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
BiocManager, Biobase, utils, methods, RSQLite,
AnnotationForge, devtools, dplR, stringr, graphics, stats,
affxparser, data.table
shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,
clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,
survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,
BiocParallel
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics,
stats, utils
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
graphics, grDevices, methods, stats, tcltk, utils, xtable
BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>=
1.31.10), GenomicFeatures (>= 1.31.5), Biostrings,
VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28),
GenomeInfoDb, Biobase
biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools,
ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats,
tibble, utils
utils, GenomicRanges, org.Hs.eg.db, BiocGenerics,
GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer
utils, methods, stats, Biobase, BiocGenerics
BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival
snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab,
FactoMineR, plspm, IRanges, GenomicRanges,
data.table,grDevices, graphics,stats, utils, methods
plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods,
grDevices, stats, graphics
igraph, snow, ape, grDevices, graphics, stats, utils,
data.table
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
Biobase, MASS, graphics, stats, survival, limma
Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges,
IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate,
data.table, dplyr, foreach, graphics, grDevices, igraph,
Matrix, methods, reshape2, stats, utils
gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats
data.table, dplyr, graphics, networkD3, RColorBrewer,
SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle,
org.Rn.eg.db
Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table,
GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>=
1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute,
IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix,
plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern,
rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14)
stats, stats4, utils, RCurl, GenomeInfoDbData
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
stats, httr, xml2, jsonlite, utils, rlang, readr,
GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment,
S4Vectors, tibble
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>=
1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25),
VariantAnnotation (>= 1.27.9), GenomeInfoDb
Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges,
BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb,
ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>=
0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils,
grDevices
grDevices, stats, utils, plyr, gridExtra, sjstats, parallel,
ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings,
BSgenome, GenomeInfoDb, AnnotationHub
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4
S4Vectors (>= 0.23.18), GenomeInfoDb (>= 1.1.3), IRanges (>=
2.5.12), methods, graphics
ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
rstan (>= 2.17.3), ranger, parallel, foreach, doParallel,
e1071, Biostrings, rPref
AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField,
GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0),
grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5),
plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils,
viridis, data.table, BSgenome, grDevices, GenomeInfoDb,
VariantAnnotation
httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel,
parallel, foreach, reshape2, dplyr
limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges,
Matrix, AnnotationDbi, digest, GenomicRanges,
SummarizedExperiment
grid, grDevices, graphics, stats, utils, gridExtra, scales,
reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase,
S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>=
1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment,
Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>=
1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer
(>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi,
GGally, ensembldb (>= 1.99.13), AnnotationDbi,
AnnotationFilter, rlang
plyr, scales, data.table, RColorBrewer, gridExtra, rlang
methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff,
Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation,
hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators,
Biostrings, ROCR, biglm, ggplot2, reshape2
ape, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods,
purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio (>=
1.8.0), utils
methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices,
stats, utils, IRanges (>= 2.13.12)
Biobase, changepoint, data.table, genefilter, graphics,
GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats
DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats,
methods, graphics, grDevices, xtable, tools, brew, stringr,
RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
edgeR, grDevices, jsonlite, methods, stats, S4Vectors, utils
SummarizedExperiment, STRINGdb, biomaRt, futile.logger,
sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2,
survminer, reshape2, stats, stringr, rlang, parallel, methods,
loose.rock (>= 1.0.12)
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>=
0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3),
Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase,
BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel
AnnotationDbi, ape, bnlearn, Category, DT, gRbase, GSEABase,
gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, reshape2, shiny,
WGCNA, data.table, grDevices, graphics, stats, utils
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI,
SparseM
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
mgcv, graphics, stats, utils, AnnotationDbi,
GO.db,BiocGenerics
org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL,
graph, Matrix, corpcor, Rcpp
AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils
methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>=
1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz
plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable
BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools,
ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils,
stats, GenomeInfoDb
igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi,
grDevices, stats, utils, GenomicRanges, IRanges
Deriv, DescTools, digest, pryr, stringr, BiocGenerics
GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors,
BiocGenerics, foreach, doParallel, bit, ff, rtracklayer,
ffbase, GenomicFiles, SummarizedExperiment
methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges,
SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs,
gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures,
ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc,
beeswarm, HardyWeinberg, graphics, stats, utils, shiny, plotly,
erma, ggbeeswarm
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics,
KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods,
rappdirs, S4Vectors, stats, utils
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4),
geneplotter, shiny, shinythemes
circlize (>= 0.3.3), GetoptLong, grDevices, utils
BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno,
data.table, matrixStats, BSgenome, parallel, IRanges (>=
2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma
XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice,
RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5),
Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>=
1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8),
Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats
(>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>=
1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8)
methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures,
Biostrings, Rsamtools, rtracklayer, AnnotationDbi, utils
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth
GWASTools, survival, VariantAnnotation, parallel, matrixStats,
SummarizedExperiment, stats, utils, SNPRelate
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
1.99.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
BiocFileCache, S4Vectors, curl, googleAuthR, httr, jsonlite,
methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr,
utils
S4Vectors, vctrs, curl, httr, jsonlite, methods, plyr, rlang,
tibble, tidygraph, utils
utils, tools, Matrix, BiocGenerics (>= 0.32.0), S4Vectors,
IRanges
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2,
scales, methods
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, GenomeInfoDb, GenomicRanges, stats, IRanges,
grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel,
R.utils, readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq,
KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
methods, utils, HilbertVis, png, grDevices, circlize (>=
0.3.3), IRanges, GenomicRanges, polylabelr
R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges,
S4Vectors, XVector, Biostrings, GenomicFeatures,
BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices,
stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
coin, stats, limma, grDevices, utils, graphics,
preprocessCore, servr, DelayedArray, matrixStats, methods,
S4Vectors
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, GenomeInfoDb
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi,
biomaRt, RankProd
edgeR (>= 3.9.14), DESeq2 (>= 1.10.1), DESeq (>= 1.22.1),
BiocParallel (>= 1.4.3), Biobase, utils, stats, grDevices,
graphics, methods
shiny, ssrch, S4Vectors, SummarizedExperiment, utils
ggplot2, ggforce, DT, R6, magrittr, dplyr, purrr, stats,
scales, rlang, openxlsx, msigdbr, kableExtra, rmarkdown, gh,
igraph, visNetwork
methods, grid, graph, hypergraph, Rgraphviz, stats4
irlba, stats, cluster, graphics, SummarizedExperiment,
BiocParallel
stats, utils, methods, graphics, grDevices, ggplot2,
GenomicFeatures, ShortRead, BiocParallel, Biostrings,
S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments,
GenomicRanges, rtracklayer, SummarizedExperiment,
VariantAnnotation, limma, edgeR, csaw, DESeq2,
TxDb.Dmelanogaster.UCSC.dm6.ensGene
stats, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d, utils
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2,
ggplot2 (>= 2.0.0), scales, ROCR, dplyr, DT, limma, methods,
UpSetR
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, ggplot2 (>= 2.0.0), d3heatmap, pheatmap,
pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma,
GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0),
shinydashboard, shinyBS, DT, rentrez, rintrojs, ggrepel, knitr,
rmarkdown, shinyAce, BiocParallel, grDevices, base64enc,
methods
biomaRt, ENVISIONQuery, AffyCompatible, R.methodsS3, utils
dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>=
1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1),
grDevices, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>=
1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats,
stringr (>= 1.3.1), utils
methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo,
rtracklayer, VariantAnnotation, randomcoloR
methods, slam, lpsymphony, fdrtool, BiocGenerics
tools, Biobase, hwriter, methods, vsn, stats, utils, e1071
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats,
ggfortify, grDevices, methods, Matrix, utils, graphics,
gridExtra, grid, lattice, Rsamtools, survival, BiocParallel,
GenomicAlignments, parallel
d3heatmap, shinyBS, shinyFiles, shinythemes, ggplot2
STRINGdb, Biostrings, igraph, graphics, utils, seqinr
utils, R6, data.table, curl, httr, Rlabkey (>= 2.3.1),
Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots,
plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown,
preprocessCore, flowCore, flowWorkspace, digest
Biobase, BiocParallel, ComplexHeatmap, circlize, compiler,
cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods,
S4Vectors, stats, SummarizedExperiment, utils
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, Matrix, fastcluster, dplyr,
HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, reshape,
rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics,
SummarizedExperiment, SingleCellExperiment, tidyr, parallel,
coda, gridExtra, argparse
AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr,
preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma,
BiocParallel
pROC, deSolve, rootSolve, KernSmooth, gdata, GenomicFeatures,
GenomicRanges, IRanges, BiocGenerics, GenomicAlignments,
Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem,
SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, methods,
Matrix, Rcpp
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
seqLogo, Biostrings, GenomicFeatures, IRanges, seqinr,
graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL,
GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2
Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr,
S4Vectors, IRanges, GenomicRanges, SummarizedExperiment,
methods
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
colourpicker, igraph, vipor, mgcv, reshape2, rentrez,
AnnotationDbi, graphics, grDevices, viridisLite, cowplot,
scales, dplyr
dplyr, magrittr, methods, quadprog, readr, readxl, stringr,
tibble, tools, utils, pracma, WriteXLS
IsoCorrectoR, readxl, tcltk2, tcltk, utils
methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>=
2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer,
rtracklayer, VennDiagram, DBI, grDevices, graphics, stats,
utils, GenomeInfoDb, grid, tximport (>= 1.7.1), edgeR,
futile.logger, stringr, dplyr, magrittr, readr, XVector
Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer,
Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg
AnnotationDbi, assertive.sets, BiocGenerics, Biobase, broom,
cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr,
GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid,
grDevices, graphics, GGally, limma, methods, RColorBrewer,
readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
magrittr, graphics, utils, GenomicRanges, SummarizedExperiment
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify,
grDevices, methods, Matrix, BiocParallel,utils, stats
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
DESeq2 (>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase
(>= 2.30.0), locfit, BiocGenerics (>= 0.7.5), BiocParallel,
genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges,
regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics,
memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase,
digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi,
grDevices, VariantAnnotation
methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
utils, apcluster
methods, XML (>= 2.3-0), graph, utils, RCurl
AnnotationDbi,graph,DBI, graph, grDevices, methods, stats,
tools, utils
data.table, BiocParallel, sqldf, stats, grid, grDevices
aod, Biobase, DESeq2, DSS, ggplot2, gplots, graphics,
grDevices, matrixStats, stats, utils, foreach, doParallel,
parallel
stringr, factoextra, kernlab, ggplot2, reshape2, gplots,
caret, RCurl, XML, class, praznik, R.utils, e1071,
randomForest, httr, jsonlite, sva (>= 3.30.1), cqn (>= 1.28.1),
edgeR (>= 3.24.3), biomaRt (>= 2.38.0), limma (>= 3.38.3),
arrayQualityMetrics (>= 3.38.0), tximport (>= 1.10.1),
tximportData (>= 1.10.0), rhdf5 (>= 2.26.2), Biobase, multtest,
pathview (>= 1.22.3), grDevices, graphics, stats, utils
Biobase, graphics, grDevices, methods, stats, tools, utils
Matrix, snpStats, VariantAnnotation, GenomeInfoDb, httr,
BiocGenerics, ensembldb, EnsDb.Hsapiens.v75, Rsamtools,
GenomicFiles (>= 1.13.6), BiocGenerics (>= 0.25.1)
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
grDevices, graphics, stats, utils, methods
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
Rcpp (>= 0.11.0), DOSE, ggtree, gridExtra, ape, grid, png,
Biobase, sva, reshape2, utils, grDevices, org.Hs.eg.db,
clusterProfiler, ggplot2, ReactomePA
BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2,
gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer,
SingleCellExperiment, splines, stats, SummarizedExperiment,
utils
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan,
mclust, apcluster, ggplot2, ellipse, limma, utils, statmod,
MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo,
stats, amap, Rtsne, gmodels
methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
tidyr, forcats, ggplot2, limma, fgsea, ropls, magrittr
Biobase, graphics, grDevices, methods, stats
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
grid, SQUAREM, LaplacesDemon, stats, graphics, utils, ggplot2,
gridBase, Biostrings
Matrix, penalized, graphics, grDevices, stats
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
DelayedArray, GenomicRanges, HDF5Array, Matrix, stats,
stringr, utils
cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer,
methods, LowMACAAnnotation, BiocParallel, motifStack,
Biostrings, httr, grid, gridBase
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures,
GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv,
KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS,
graphics, stats, stats4, methods
BiocGenerics, stats4, graphics, stats, utils, MASS, Biobase,
quantreg, limma, affy, SparseM, vsn, zlibbioc
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel,
foreach, doParallel, matrixcalc, dendextend, sigclust, Rtsne,
survival, corpcor, umap
parallel, Rcpp, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment, BiSeq
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods
Biobase, graphics, grDevices, methods, stats, utils
robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony,
pscl, pbapply, car, dplyr, vegan, chemometrics, ggplot2,
pheatmap, cplm, logging, data.table, lmerTest, hash, optparse,
MASS, MuMIn, grDevices, stats, utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors,
methods, preprocessCore, GenomicAlignments, Rsamtools,
Biostrings, GenomicRanges, IRanges, VariantAnnotation,
SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics,
stats, grDevices, utils, zlibbioc, vcfR
data.table, RColorBrewer, methods, wordcloud, grDevices,
survival
clusterProfiler, DOSE, enrichplot, gridExtra, biomaRt, sva,
ggsci, ggplot2, ggrepel, ggpubr, data.table, pheatmap, png,
grDevices, grid, stats, utils, dendextend, scales, Biobase,
msigdbr, KEGGgraph, KEGGREST, graph, graphics, pathview, XML
Biobase, affy, methods, stats, utils, zlibbioc
multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi,
methods, parmigene,igraph,reactome.db
dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats,
utils, IRanges, methods, BiocGenerics, parallel, data.table
Biobase, graphics, grDevices, venn, mclust, stats, MASS
Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr,
stringr, abind, methods, parallel, reshape2, stats, stats4,
graphics, utils, SummarizedExperiment(>= 1.5.3), progress
methods, TFBSTools, IRanges, XVector, Biostrings
BiocGenerics, ProtGenerics, digest, irlba, utils
methods, DelayedArray, Rcpp, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix
stats, graphics, utils, limma (>= 3.30.13),
SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0),
BiocFileCache, rappdirs, rpx, xml2, RCurl, ggplot2, reshape2,
PairedData
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6),
RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics,
grDevices, stats, utils
biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2,
graphics, grDevices, Gviz, IRanges, limma, parallel, S4Vectors,
stats, SummarizedExperiment, utils
AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
GenomicRanges, limma, DMRcate, vegan, BiocGenerics, minfi,
IRanges, S4Vectors, methods, parallel, ggplot2 (>= 2.0.0),
permute, Gviz, missMethyl, isva, SummarizedExperiment,
SmartSVA, graphics, stats, utils, matrixStats
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
data.table, parallel, ROCR, matrixcalc, clues, ggplot2,
doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm,
truncnorm, assertthat, BiocStyle, stats, utils
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, GOSemSim (>=
1.99.3), MeSH.db, methods, rvcheck, utils
methods, stats, utils, fdrtool, MeSH.db, MeSH.AOR.db,
MeSH.PCR.db, MeSHDbi, MeSH.Hsa.eg.db, MeSH.Aca.eg.db,
MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db, cummeRbund, org.Hs.eg.db,
Category, S4Vectors, BiocGenerics, RSQLite
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75,
stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi,
MWASTools, mygene
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb,
GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP,
matrixStats, purrr, data.table, magrittr, methods, utils,
ensembldb, EnsDb.Hsapiens.v86, stringr
rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges,
ggplot2, Rsamtools, DBChIP, purrr, data.table, methods, dplyr,
magrittr
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench, IHW
beanplot (>= 1.2), GenomicRanges (>= 1.34.0), gplots (>=
3.0.1), Matrix (>= 1.2), matrixStats (>= 0.54), Rcpp,
RColorBrewer (>= 1.1), stats (>= 3.4), SummarizedExperiment (>=
1.12), utils (>= 3.4)
edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots,
corrplot, vsn, brew, rjson, log4r
epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan,
GenomeInfoDb, phyloseq, httr
methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot,
parallel, metafor, metap, rlang, topconfects, grDevices,
graphics, stats, htmlwidgets
methods, utils, stats, S4Vectors, bsseq, DSS, methylKit,
DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
methylKit, GenomicRanges, GenomeInfoDb, parallel,
BiocGenerics, S4Vectors, methods, stats, IRanges, msm
DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats,
parallel, methods, ggplot2, matrixStats, graphics, stats, utils
Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges,
stats, utils
grDevices, stats, utils, lumi, methylumi, Gviz, genoset,
SummarizedExperiment, IRanges, GenomicRanges,
VariantAnnotation, rtracklayer, GenomicFeatures, annotate,
Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt,
methods, parallel
Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase,
grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr,
minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter,
genefilter, methods, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, shiny,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors,
methods, parallel, ggplot2, gridExtra, rebus
IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>=
0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools,
gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils,
limma, grDevices, graphics, stats, utils
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table,
GenomeInfoDb, S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, Biobase, graphics, lattice, annotate,
genefilter, AnnotationDbi, minfi, stats4, illuminaio
stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat,
dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors,
BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb,
bumphunter, IRanges, limma, minfi
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
dplyr, reshape2, Rtsne, scales, stats, tidyr, utils, vegan
graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply,
stats
AnnotationDbi, Biobase, BiocParallel, compiler, data.table,
edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph,
graphics, grDevices, grid, GSEABase, ismev, limma, matrixStats,
org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils,
vegan
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, Formula, data.table, pracma, MCMCpack, coda, modeest,
testthat, Rcpp, scales,
S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges,
beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma,
preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>=
1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog,
data.table, GEOquery, stats, grDevices, graphics, utils,
DelayedArray (>= 0.9.8), HDF5Array, BiocParallel
methods, BiocGenerics, Biobase, S4Vectors (>= 0.23.18),
IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff,
foreach, matrixStats, lattice, data.table, grid, stats, utils
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
ggplot2, Biobase, stats, bsseq, methods
utils, methods, graphics, KernSmooth, stats
graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi,
Rgraphviz
methods, stats, utils, RCurl, httr, stringr, Hmisc, energy,
entropy, Roleswitch, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
heatmap.plus, InvariantCausalPrediction, Category, GOstats,
org.Hs.eg.db
DBI, RSQLite, stringr, sqldf, plyr, methods
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL,
NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd,
BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust,
SOMbrero, ppclust, miRspongeR, Rcpp, utils,
SummarizedExperiment, GSEABase, org.Hs.eg.db,
MatrixCorrelation, energy
corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA,
DOSE, survival, grDevices, graphics, stats, varhandle,
linkcomm, utils, Rcpp, org.Hs.eg.db
graphics, grDevices, gridExtra, Matrix, parallel,
RColorBrewer, reshape, scales, utils
limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest,
statmod, ruv, stringr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db,
AnnotationDbi, BiasedUrn, GO.db,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, utils
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats
rstan (>= 2.17.3),rstantools (>=
1.5.0),MASS,Matrix,stats4,ggplot2
methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment,
plyr, foreach, utils, sSeq, xtable
ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation,
BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb,
GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools,
magrittr, methods, grDevices, graphics, stats, utils, stringr,
data.table
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr,
cowplot, utils, stats, grDevices
cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice,
naturalsort, snowfall, stats4, tsne, methods, graphics, stats,
utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats,
grDevices
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, assertive, BiocGenerics, GenomicRanges, S4Vectors,
IRanges, XVector, stringi, stringr
rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2,
ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot,
ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach,
reticulate, grDevices, stats, utils
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>=
0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>=
2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS,
reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr,
proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>=
0.12.0)
parmigene, randomForest, SummarizedExperiment, gplots,
circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase,
limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats,
RISmed, grid, utils
MASS, splines, lattice, IRanges, GenomicRanges,
GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors
HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi,
lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble,
tidyr, ggplot2, Biobase, IRanges, S4Vectors
methods, compiler, grDevices, grImport, stringr, BiocGenerics,
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
Biostrings, BSgenome, rtracklayer, VariantAnnotation,
BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue,
SummarizedExperiment
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
XML, scales, htmlwidgets,grDevices, stats, stats4, graphics,
utils, ggplot2
methods, stats, grid, S4Vectors, IRanges (>= 1.13.5),
Biostrings, lattice, rGADEM, utils
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
BSgenome, easyRNASeq, edgeR, GenomicAlignments,
GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges,
parallel, plyr, Rsamtools, R.utils, stats,
SummarizedExperiment, S4Vectors, utils
shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools
BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn,
grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16),
mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS,
Rcpp
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite,
uuid, jsonlite
lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel,
preprocessCore, reshape2, survival, statmod, minpack.lm, utils,
grDevices, graphics, stats, doSNOW, snow, foreach, data.table,
MASS, dplyr, tidyr, broom, purrr, stringr
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr,
RecordLinkage, grid
ggplot2, BiocParallel, caret, gridExtra, reshape2, stats,
utils, grDevices, graphics, MSstats
limma, lme4, lmerTest, dplyr, tidyr, statmod, methods,
reshape2, data.table, matrixStats, stats, utils, ggplot2,
grDevices, graphics, MSstats
xml2, utils, gmapR, methods, IRanges, Biobase, circlize,
jsonlite, graphics, Rsamtools, grDevices, Biostrings,
rtracklayer, VariantTools, Homo.sapiens, BiocGenerics,
GenomicRanges, GenomicFeatures, SummarizedExperiment
graphics, grDevices, stats, methods, fields
methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors
(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman,
limma
data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman,
pheatmap, methods, metap, GenomicRanges, graphics, stats,
utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, parallel, doParallel, foreach, grDevices, graphics,
utils, SummarizedExperiment, stats
BiocParallel, blme, ComplexHeatmap, data.table, DESeq2,
doParallel, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid,
limma, lmerTest, lme4, magrittr, Matrix, matrixStats, methods,
parallel, progress, purrr, reshape2, scales, sctransform,
stats, SingleCellExperiment, SummarizedExperiment, S4Vectors,
tibble, variancePartition, viridis
stats, parallel, S4Vectors, BiocGenerics (>= 0.18.0),
VariantAnnotation (>= 1.18.1), reshape2 (>= 1.4.1), plyr (>=
1.8.3), ggplot2 (>= 2.1.0), pracma (>= 1.8.8),
SummarizedExperiment (>= 1.2.2), IRanges (>= 2.6.0),
GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>=
0.1-20), cowplot (>= 0.9.2)
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf,
plyr
httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
graphics, methods, baseline, signal, GenomicAlignments,
GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils,
Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot,
csaw
hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats,
grDevices, graphics, stringr, knitr, testthat, utils,
AnnotationDbi, httr, org.Hs.eg.db, rtracklayer
BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
fda, CSAR, ICSNP
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2
boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod,
plotrix, limma
Rcpp (>= 0.11.0), minet, GENIE3, c3net, PCIT, GeneNet, tools,
pracma, Matrix, corpcor, fdrtool
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
R.utils
glasso, mvtnorm, parcor, GeneNet, huge, CompQuadForm, ggm,
mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
dmt, ggplot2, graph, igraph, parallel, plyr, qvalue,
RColorBrewer
entropy, SummarizedExperiment, SingleCellExperiment, Matrix,
cluster, data.table, stats, methods, DelayedArray, HDF5Array
Biostrings, checkmate, dplyr (>= 0.8.0), FactoMineR, ggdendro,
grDevices, grid, kableExtra, lubridate, methods, pander,
parallel, plotly, readr, reshape2, rmarkdown, Rsamtools,
scales, ShortRead, stats, stringr, tidyr, tidyselect (>=
0.2.3), truncnorm, utils, viridisLite, XVector, zoo
graphics, grDevices, marray, methods, nnet, stats
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment,
matrixStats, ggforce
methods, stats, utils, grDevices, parallel, GenomeInfoDb,
GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2),
bamsignals (>= 1.4), rtracklayer (>= 1.32)
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
Biobase, BiocGenerics, Biostrings, GenomeInfoDb,
GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr,
ggplot2, magrittr, parallel, stats, utils
multtest (>= 1.7.3), graphics, grDevices, stats, akima
affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1),
ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>=
1.0.0), splines, stats, stats4, utils, zlibbioc
BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocManager, utils, S4Vectors (>=
0.9.25), RSQLite, DBI
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
compositions, DT, grDevices, knitr, jsonlite, matrixStats,
rmarkdown, shiny, stats, vegan, zCompositions
stats, utils, grDevices, graphics, methods, rexposome, limma,
sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet,
SmartSVA, isva, parallel, SummarizedExperiment, stringr
SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2,
BiocParallel, parallel, grDevices, graphics, stats, utils,
methods, BiocGenerics
HelloRanges, fpc, stats, MultiAssayExperiment, pdftools,
methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown,
kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2,
ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR,
PerformanceAnalytics, tidyr, data.table, cluster, magick
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
GEOmetadb, RSQLite, data.table, methods, tools, utils,
AnnotationDbi, RCurl, stats, DT, data.table, knitr, Rtsne,
dendextend, clusteval, ggplot2, ggfortify
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, nem
Rtsne, plotly, gplots, grDevices, graphics, stats, utils,
methods, flowCore
Biobase, S4Vectors, methods, AnnotationDbi, stats, utils,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr
methods,Biobase,BiocGenerics,gtools,flowCore(>=
1.31.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>=
3.33.1),flowStats(>= 3.29.1),flowClust(>=
3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp
limma, stats, reshape, ggplot2, grDevices, RColorBrewer,
pheatmap, knitr, methods, devtools
Biobase, graphics, methods, stats, twilight
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, methods, tools, utils,
BiocFileCache, DBI, dbplyr
Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph,
IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats
BBmisc, Biobase, BiocGenerics, compiler, DESeq2 (>= 1.16.1),
GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, gplots,
graphics, IRanges, matrixStats, plotly, plyr, pcaMethods,
PRROC, RColorBrewer, Rcpp, reshape2, S4Vectors, scales,
splines, stats, utils
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGG.db, nlme
SummarizedExperiment, S4Vectors, stats, methods, abind,
BiocParallel
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb,
grDevices
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph,
stats, utils
stats, utils, dplyr, rlang, iterators, parallel, foreach,
doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges,
S4Vectors
limma, corpcor,matrixStats, reshape2, scales, ggplot2,
rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats,
methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2,
ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet,
gmodels, ROCR, RColorBrewer, knitr, devtools, ape
EMT, mclust, Matching, data.table, stats, grDevices, graphics,
utils
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
KEGGREST, methods, utils
lars, methods, parallel, stats, survival, utils
goseq, Biobase, DOSE, reshape2, igraph, org.Hs.eg.db,
org.Mm.eg.db, BiocGenerics, AnnotationDbi, JunctionSeq,
BiasedUrn, GO.db,gdata, geneLenDataBase, grDevices, graphics,
stats, utils, VennDiagram, RColorBrewer, ensembldb,
AnnotationHub, S4Vectors, dplyr, plotly, webshot, htmlwidgets ,
mgcv ,gridExtra, grid ,gplots, tibble , EnrichmentBrowser,
annotate , KEGGREST
utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr
cleaver (>= 1.3.6), Biobase, Biostrings (>= 2.47.5), IRanges
(>= 2.13.11), S4Vectors (>= 0.17.24), mzID, mzR (>= 1.99.1),
MSnbase (>= 1.15.5), Pviz, biomaRt, GenomicRanges (>= 1.31.7),
rtracklayer (>= 1.39.6), ensembldb (>= 1.99.13), BiocParallel,
AnnotationFilter
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, genefilter, ggplot2 (>= 2.0.0), d3heatmap, scales,
NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny
(>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce,
threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr,
grDevices, methods
methods, stats, utils, Matrix, DelayedMatrixStats,
DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng
AnnotationDbi, Biobase, Category, GO.db, graph, graphics,
GSEABase, KEGG.db, methods, ScISI, stats, stats4
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph,
foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid,
utils, graphics, scales, magrittr, formula.tools, rlang
S4Vectors (>= 0.9.25), Rsamtools (>= 1.10.2), GenomicFeatures
(>= 1.19.8), biomaRt (>= 2.17.1), stringr, RCurl, Nozzle.R1,
VariantAnnotation (>= 1.7.28), rtracklayer, RSQLite, ggplot2,
AnnotationDbi, customProDB (>= 1.21.5), pheatmap, dplyr,
processx, readr, seqinr
ggplot2, protolite, Biobase, GEOquery, Rook, htmltools,
httpuv, jsonlite, limma, opencpu, assertthat, methods, httr,
rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite,
gtable, stats, Matrix, Matrix.utils, pheatmap, scales, ccaPP,
grid, grDevices, AnnotationDbi
Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
methods, downloader, stats, utils, graphics, grDevices, lsa,
reshape2
SingleCellExperiment, RColorBrewer, igraph, transport, pracma,
cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree,
pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics,
stats, utils, cowplot, S4Vectors, BiocGenerics,
SummarizedExperiment, Biobase, phateR
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, Hmisc, gplots, Category, AnnotationDbi,
hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
SNPchip, hgu133a.db, HTSanalyzeR, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply,
RColorBrewer, shiny, shinyBS, shinyjs, OmaDB, plyr, xml2, zoo
Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales,
grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice,
caret, plot3D, stats
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
methods, stats4, IRanges, GenomicRanges, graphics, grDevices,
stats, Rsamtools, GenomicAlignments, S4Vectors
bnlearn (>= 4.4.1), C50 (>= 0.1.2), MASS, matrixStats,
partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore,
grDevices, graphics, stats, utils, parallel, pheatmap (>=
1.0.8), dplyr, gdata
methods, PICS, graphics, grDevices, stats, Gviz, fda,
BSgenome, stats4, BiocGenerics, IRanges, S4Vectors
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
GenomeInfoDb, parallel, stats, utils
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray,
methods, quadprog, Rcsdp, stats, stats4, utils
methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>=
1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb,
Rsamtools, S4Vectors (>= 0.23.10), utils
Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils,
Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges,
Biostrings, BSgenome (>= 1.32.0)
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma,
zlibbioc
stats, CompQuadForm, Matrix, survival, Biobase, GSEABase
DESeq2, ROTS, vsn, stats, utils, methods, gridExtra, MASS,
data.table, ggplot2, Biobase, S4Vectors, BiocParallel
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, tcR, truncdist, vegan, VGAM
Biobase, Category, graph, graphics, grDevices, lattice,
methods, RColorBrewer, stats
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
Biobase, BiocGenerics, graphics, grDevices, grid, MASS,
methods, RColorBrewer, rrcov, stats4, utils
methods, BiocParallel, tools, utils, data.table (>= 1.11.8),
GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6),
BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0),
GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>=
1.32.3), S4Vectors (>= 0.18.3)
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, GenomeInfoDb, S4Vectors
graphics, grDevices, stats, utils, methods, cgdsr, parallel,
stringr, reshape2, data.table, RColorBrewer, BiocParallel,
magrittr, biomaRt, XML, httr, jsonlite, ggplot2, ggrepel, grid,
S4Vectors, IRanges, GenomicRanges, LowMACAAnnotation,
googleVis, shiny, shinyBS, DT, brglm, matrixStats
diagram, stringr, ggplot2, reshape2, grDevices, matrixcalc,
stats, gplots, methods, utils, graphics
Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2,
grDevices, lazyeval, lubridate, magrittr, pheatmap,
preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang,
scales, stats, sva, tidyr, tibble, tools, utils, viridis,
wesanderson, WGCNA
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
stats, graphics, utils, grDevices, methods, pracma, Biobase,
minpack.lm, BiocParallel, missForest, ropls
GenomicRanges, stats, soGGi, methods, utils, S4Vectors,
R.utils, dplyr, magrittr, tidyr, IRanges, rjson,
ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT,
pheatmap, EnrichedHeatmap, ComplexHeatmap, grid, circlize,
BiocParallel, rtracklayer, GenomeInfoDb
methods, cluster, stats, limma, CoGAPS, NMF, ROCR
Biobase, mclust (>= 4.3), caret, e1071, sampling, class,
kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin,
BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS,
knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr,
ggplot2, biomaRt, utils, grDevices, graphics
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.18.1), DAPARdata (>= 1.16.0), rhandsontable,
data.table, shinyjs, DT, shiny, shinyBS, shinyAce, highcharter
(>= 0.7.0), htmlwidgets, webshot, R.utils, shinythemes,
XML,later, rclipboard, shinycssloaders, future, promises,
colourpicker, BiocManager, shinyTree, shinyWidgets, sass,
tibble
mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils,
Biobase, BiocManager, RCurl
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel,
rpx, tidyr, dplyr, plotly, rmarkdown,
AnnotationDbi, AnnotationHub, BiocFileCache, cluster,
colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR,
fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices,
highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma,
miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils,
reshape2, shinyjs, stringr, stats, SummarizedExperiment,
survival, tools, utils, XML, xtable, methods, org.Hs.eg.db
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, BiocManager, Biobase, labeling, GO.db
robustbase, methods, R.utils, taRifx, S4Vectors,
SummarizedExperiment, ggplot2, ggridges, stats, utils, UpSetR,
cowplot, grid, MuMIn
Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
S4Vectors, data.table, grDevices, graphics, stats, utils,
SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools,
Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra,
futile.logger, VGAM, tools, methods, rhdf5, Matrix
biovizBase, Biostrings, GenomicRanges, IRanges, data.table,
methods
data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots,
Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub,
GenomicRanges, graph, grDevices, stats, utils
doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2,
parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter,
stats, grDevices, methods, utils, graphics, pwrEWAS.data
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang,
RSeqAn
Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander,
S4Vectors
methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>=
1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
tidyr, preprocessCore, limma, ggplot2, RColorBrewer, stats,
utils, Biostrings, GenomicRanges, IRanges, graphics,
BiocGenerics, stringr, purrr, tibble, ggdendro, grDevices,
dplyr, magrittr, assertthat
reshape, ggplot2, Biostrings, biovizBase, graphics, methods,
plyr, stats
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel
SummarizedExperiment, utils, sva, stats, methods, graphics
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, BiocGenerics, S4Vectors
(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings,
BSgenome, Rsamtools (>= 1.99.1), GenomicFeatures (>= 1.17.13),
ShortRead (>= 1.19.1), GenomicAlignments, BiocParallel,
GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi
methods, parallel, clues, ggplot2, pheatmap, clValid, igraph,
data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors,
IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
ggbio
methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
utils, grDevices, graphics, stats, tools, xtable, R2HTML,
TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges
(>= 2.13.12), XVector, GenomicRanges (>= 1.31.8),
SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools,
ShortRead (>= 1.37.1)
BiocGenerics, GenomeInfoDb, IRanges, methods, S4Vectors,
stats, SummarizedExperiment
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools,
BSgenome, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
SummarizedExperiment, GenomicScores
methods, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb,
ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny,
VGAM, dplyr, reshape2
utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors (>=
0.23.19), IRanges, GenomeInfoDb, GenomicAlignments
biomaRt, AnnotationDbi, GenomicRanges,
BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0),
Biostrings, rtracklayer, org.Hs.eg.db, GenomicFeatures,
rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3),
BiocGenerics, S4Vectors, stats, plotrix, pbapply, RSQLite,
proxy, DBI, pheatmap, ggplot2, cowplot, ggseqlogo, methods,
utils
stringr, gplots, ggplot2, methods, stats, utils, shiny
plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1),
limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi,
parallel,IRanges,grDevices,aCGH
Rgraphviz, sfsmisc, graphics, methods, graph, grDevices,
flowType (>= 2.0.0)
AUCell (>= 1.1.6), BiocGenerics, data.table, feather,
graphics, GSEABase, methods, R.utils, stats,
SummarizedExperiment, utils
RColorBrewer, alabama, edgeR, reshape2, tseries, vegan, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
stats, grDevices, graphics, methods
stats, utils, methods, RCurl, rjson, foreach, doParallel,
Biostrings, GOSemSim, ChemmineR, fmcsR, rcdk (>= 3.3.8)
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools
dplyr, rappdirs, jsonlite, methods, utils, tximport
httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph,
stats, graph, R.utils
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
jsonlite, httr, progress, ggplot2, methods
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph,
reactome.db, igraph, graphite
assertive.base (>= 0.0-7), assertive.files (>= 0.0-2),
assertive.numbers (>= 0.0-2), assertive.properties (>= 0.0-4),
assertive.sets (>= 0.0-3), assertive.types (>= 0.0-3), Biobase
(>= 2.34.0), data.table (>= 1.10.4), dplyr (>= 0.5.0), magrittr
(>= 1.5), openxlsx (>= 4.0.17), pathological (>= 0.1-2),
reshape2 (>= 1.4.2), stats, stringi (>= 1.1.5),
SummarizedExperiment (>= 1.4.0), testthat (>= 1.0.2), tidyr (>=
0.6.2), utils
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocGenerics, biomaRt, circlize, graphics, grDevices, methods,
rtracklayer, plyr, stats, utils
BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno,
graphics, IRanges (>= 1.13.5), multtest, stats, utils
memoise, GenomicRanges, IRanges, BSgenome, Biostrings,
rtracklayer, parallel, graphics, stats, utils, methods,
GenomeInfoDb, S4Vectors, tools
BiocStyle (>= 2.5.19), derfinder (>= 1.1.0), DEFormats,
DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1),
knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR,
rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
readr, rtracklayer, graphics, stats, utils, methods, settings,
BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges,
GenomeInfoDb, BiocParallel, doParallel, parallel, foreach,
caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db,
impute, iterators
parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots,
grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo,
aroma.affymetrix, Rsolnp, cluster
Biobase,hwriter,Category,GOstats,limma(>=
3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db,
GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>=
1.3.41), ggplot2, ggbio, IRanges
rJava, graphics, stats, utils, grDevices
utils, stats, methods, S4Vectors, Biobase,reshape2,
AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1),
magrittr, bigrquery, ExperimentHub, AnnotationHub, rlang
methods, utils, stats, lsr, FactoMineR, stringr, circlize,
corrplot, ggplot2, reshape2, pryr, S4Vectors, imputeLCMD,
scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools,
scales, lme4, grDevices, graphics, ggrepel, mice
Biostrings, GenomicRanges, methods, graphics, seqLogo
httr, rJava, GenomicRanges, rtracklayer, data.table, utils,
plyr, xml2, methods, S4Vectors, dplyr, stats, glue,
BiocGenerics
rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
hash, AnnotationDbi
GenomicFeatures, SGSeq, GenomicRanges, methods, utils
BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2,
GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments,
ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4
graphics, stats, utils, grid, gridExtra, reshape2, gplots,
ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm,
dynamicTreeCut, sqldf, gsubfn, hash, png, sqldf, igraph,
BgeeDB, knitr, RITANdata
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb,
S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
grDevices
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr
RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid,
hwriter, lattice, latticeExtra, limma, methods, splots (>=
1.13.12)
geneplotter, limma, biomaRt, car, splots, methods
methods, stats, graphics, grDevices, grid, matrixStats,
assertive, BiocGenerics, XVector, Biostrings, BiocParallel,
GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer,
Rsamtools, BSgenome, RColorBrewer, colorRamps, biovizBase,
ggplot2, Gviz, reshape2, stringi, stringr, ROCR
methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz
methods, assertive, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, stats, ranger
methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz
Biostrings(>= 2.32.1), GenomicRanges(>= 1.16.4), IRanges(>=
2.10.5), Rsamtools(>= 1.16.1), rtracklayer(>= 1.24.2),
GenomicAlignments(>= 1.5.12), S4Vectors(>= 0.14.7), graphics,
stats, utils
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
GenomicRanges , IRanges, edgeR, DESeq, DBI
Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib,
FactoMineR, factoextra, corrplot, PerformanceAnalytics,
reshape2, DESeq2, systemPipeR, systemPipeRdata,
clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr,
pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings,
parallel
affy, boot, impute, splines, graphics, qvalue, reshape2
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
SummarizedExperiment, GenomicAlignments (>= 0.99.4),
rtracklayer, GenomeInfoDb
httr, progress, jsonlite, utils, Biobase, BiocGenerics (>=
0.23.1)
graphics, grDevices, methods, MultiDataSet, stats
BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods,
S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid,
reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools,
GenomicAlignments, GenomicFiles
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,
BiocParallel
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, assertthat, stringi, rvest, data.table, xml2, dplyr,
purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr,
scales
BiocGenerics, data.table, DelayedArray, GenomicRanges,
GenomeInfoDb, httr, IRanges, limma, methods, RaggedExperiment,
RCircos, RCurl, RJSONIO, S4Vectors (>= 0.23.10), stats,
stringr, SummarizedExperiment, survival, TCGAutils, XML
RedeR, minet, viper, mixtools, snow, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment
survival, RColorBrewer, grDevices, graphics, stats, utils,
scales, data.table, egg, ggplot2, pheatmap, dunn.test
shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2
GENLIB, gRain, snpStats, kinship2, methods, stats, utils
graphics, methods, SparseM, stats, utils
methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0)
methods, reshape2, scales, gridExtra, XML
Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph,
rmarkdown, knitr, SummarizedExperiment, AnnotationDbi
graphics, stats, utils, methods, e1071, parallel, foreach,
doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR,
robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1),
SummarizedExperiment, SingleCellExperiment, BiocGenerics,
S4Vectors
SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow,
purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
BiocGenerics, SummarizedExperiment, Matrix, ggbeeswarm, grid,
DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats,
utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel
SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods
igraph, Matrix, matrixStats, BiocParallel, BiocNeighbors,
SummarizedExperiment, SingleCellExperiment, scran, scater,
data.table, dplyr, ggplot2, randomForest, graphics, methods,
stats, DelayedArray
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SingleCellExperiment, SummarizedExperiment, grDevices,
graphics, stats, S4Vectors, scran
Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook,
rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods,
nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats, dplyr, pROC
SingleCellExperiment, SummarizedExperiment, methods, stats,
bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12)
glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1),
fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel,
grDevices, graphics, stats, utils, DESeq, locfit
hexbin, stats, methods, cluster, dplyr, entropy
AnnotationDbi, GO.db, RpsiXML, annotate, methods,
org.Sc.sgd.db, utils
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
BiocParallel, BiocSingular, cluster, DelayedArray,
DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel,
pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv,
S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3),
SummarizedExperiment
knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges,
reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15),
annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb,
Biostrings, DT, HDF5Array (>= 1.7.5)
SingleCellExperiment, SummarizedExperiment, stats, methods,
graphics, grDevices, parallel, quantreg, cluster, moments,
data.table, BiocParallel, S4Vectors, ggplot2, forcats,
BiocGenerics
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, edgeR, fpc, gplots, grDevices,
hexbin, limma, matrixStats, mixtools, RColorBrewer, boot,
rhdf5, RUVSeq, rARPACK
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
Biostrings, methods, snpStats, VariantAnnotation,
GenomicRanges, BiocParallel, graphics, SummarizedExperiment
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, BiocParallel, elasticnet, cluster, kernlab, origami
Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3),
reshape, BiocGenerics, robustbase, scales, utils, stats,
S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db,
org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr,
GenomicRanges, magrittr, glue
SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel,
Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma,
BiocNeighbors, igraph, statmod, DelayedArray,
DelayedMatrixStats, BiocSingular, dqrng
stats, utils, methods, graphics, doParallel, foreach,
parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS
(>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>=
4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>=
1.3.0), BiocParallel (>= 1.12.0)
data.table, GenomicAlignments, GenomicFeatures, GenomicRanges,
Rsamtools, ShortRead, parallel, plyr, BiocGenerics,
BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods,
ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio,
rtracklayer, SingleCellExperiment, SummarizedExperiment
sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer
methods, RSQLite, igraph, S4Vectors, plotly, reactome.db,
AnnotationDbi, SummarizedExperiment, SingleCellExperiment,
nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud,
rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices,
graphics, stats, utils, outliers, Category, meshr, GOstats,
ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork
GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly,
tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr,
S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor,
methods, scales, msigdbr
Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils,
abind
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>=
2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods,
rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2),
stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils
Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr,
methods, rvcheck, utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
methods, IRanges, BSgenome, digest, rtracklayer,
GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite,
plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class,
S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>=
0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager
data.table, eulerr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, grDevices, grid, IRanges, limma, methods,
parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer,
S4Vectors, stats
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, Biobase, gdsfmt,
GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf,
Matrix, dplyr, rlang, tidyr
BiocParallel, R6, grDevices, utils, illuminaio, MASS,
GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors,
randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy
SummarizedExperiment, data.table, pheatmap, seriation,
ComplexHeatmap, circlize, methods
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, dplyr
AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>=
2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>=
1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19),
grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7),
stats
Rcpp, methods, stats, xptr, BiocGenerics
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter,
methods, zlibbioc, lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC,
PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot
corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS,
penalized, quadprog, snowfall, stats
biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer,
Matrix, SparseM, graphics, stats, utils, SummarizedExperiment,
BiocParallel, methods
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase,
DelayedArray
BiocGenerics, Biostrings, class, graphics, grDevices,
GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats,
utils, PMCMR
graph, igraph, RBGL, graphics, utils, stats, methods
quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0),
VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb,
GenomicRanges, rtracklayer, SummarizedExperiment, graphics,
stats, utils
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma
graphics, stats, gbm, Hmisc, GenomicRanges, methods
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
S4Vectors (>= 0.23.19), methods, BiocGenerics, utils, stats
ape, colourpicker, cluster, ComplexHeatmap, data.table,
DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA (>= 1.26.0),
GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly,
RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, shinyBS, sva,
reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda,
shinycssloaders, shinythemes, umap
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocNeighbors, BiocParallel, stats, utils, Rcpp, ExperimentHub
methods, stats, graphics, ggplot2, grDevices, ggrepel, plotly,
tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase,
BiocParallel, SummarizedExperiment, matrixStats, reshape2,
S4Vectors
ape, seqinr, Rcpp, methods, graphics, utils, stats
minfi, S4Vectors (>= 0.19.1), RColorBrewer
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice,
methods, stats, BiocGenerics
ape, graphics, grDevices, igraph, matrixStats, methods,
SingleCellExperiment, SummarizedExperiment
SummarizedExperiment, curl, dplyr, foreach, httr, stats,
utils, methods, readr, rhdf5, jsonlite, tidyr
magrittr (>= 1.5), matrixStats, dplyr, stats, tidyr, utils,
Rcpp (>= 1.0.0)
scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2,
reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph,
Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics,
stats, utils
aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
methods, graphics, lattice, grid, foreach, utils, Biobase,
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, oligoClasses (>= 1.31.1)
DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel,
VariantAnnotation, BiocGenerics, IRanges, methods,
SummarizedExperiment, RColorBrewer, Biostrings, grDevices,
gridExtra, stats, grid, utils, reshape2, scales, S4Vectors
methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb,
GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
rtracklayer, preprocessCore, chipseq, BiocParallel
S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio,
reshape2, NMF, pcaMethods, Biobase, methods, proxy
methods, ggplot2, scater (>= 1.13.27), shiny, jpeg, magrittr,
utils, S4Vectors
stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
methods, glmnet, parcor, huge, stats, graphics, utils
BiocGenerics (>= 0.31.6), nnlasso, nnls, parallel, data.table,
Biostrings, GenomicRanges, IRanges, BSgenome,
BSgenome.Hsapiens.1000genomes.hs37d5, GenomeInfoDb, ggplot2,
gridExtra
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges
httr, igraph, utils, stats, miRNAtap, miRNAtap.db,
AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots,
grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks,
gdata, MAGeCKFlute,networkD3
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
akima, BiocGenerics, BiocParallel, checkmate (>= 2.0.0),
edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods,
scales, scater (>= 1.13.27), stats, SummarizedExperiment,
utils, crayon, S4Vectors, rlang
annotate, Biobase, graphics, grDevices, grid, methods, utils,
XML
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, IRanges (>= 2.20.1), GenomeInfoDb,
GenomicRanges (>= 1.23.21), GenomicFeatures, Rsamtools,
GenomicAlignments, graph, Rgraphviz
graphics, ggplot2, seqLogo, Biostrings, biomaRt,
GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz,
IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods,
BSgenome.Mmusculus.UCSC.mm9, googleVis
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators,
DBI, lazyeval, methods, tools, stats, BiocGenerics, RSQLite,
tibble
graphics, grDevices, methods, RColorBrewer, stats, utils
shinyBS, ggplot2, reshape2, MASS, RColorBrewer,
gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors,
BiocGenerics, grDevices, stats, utils, graphics, shinyjs
Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb,
rtracklayer, SummarizedExperiment, IRanges, GenomicRanges,
DESeq2, Rsamtools, GenomicFeatures, GenomicAlignments,
grDevices, Gviz, BiocParallel, BiocManager, BiocStyle
GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb,
Gviz, Rsolnp
SpidermiR, graphite, AnnotationDbi, e1071, ROCR, MLmetrics,
grDevices, igraph, reshape2, ggplot2
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
dplyr, magrittr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, IRanges, Rsamtools, S4Vectors, grid,
BiocGenerics, ggplot2, reshape2, stats, gridExtra,
TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer,
gplots, hash, plotrix
methods, assertive, BiocGenerics, XVector, stringr, stringi
assertthat, Biostrings, stringr, dplyr, methods, rlang
Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra,
networkD3, ggrepel, graphics, stats, org.Hs.eg.db,
AnnotationDbi
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
S4Vectors (>= 0.23.20), IRanges (>= 2.13.16), GenomeInfoDb (>=
1.13.1)
ape, MASS, grDevices, graphics, stats, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma,
methods, stats, SummarizedExperiment, edgeR, ggplot2, limma,
lmtest, parallel, pls
data.table, reshape2, grid, ggplot2, stats, grDevices,
graphics, utils, biomaRt
SummarizedExperiment, dplyr, ggplot2, methods, stats
RColorBrewer, lattice, qvalue, multtest, utils, tools,
Biobase, knitr, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2),
rmarkdown (>= 1.0)
doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2
seqinr, methods, Biostrings, stringr, BiocGenerics
BiocGenerics, GenomicRanges, GenomicFeatures (>= 1.31.3),
SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson,
ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate,
pheatmap, batchtools, yaml
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
graphics, grDevices, methods, stats, utils, stringr,
assertthat
grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics,
reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot,
graphics, GenomicAlignments, Hmisc
downloader (>= 0.4), survminer, grDevices, dplyr, gridExtra,
graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0),
data.table, EDASeq (>= 2.0.0), edgeR (>= 3.0.0), jsonlite (>=
1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes,
survival, stringr (>= 1.0.0), IRanges, scales, rvest (>=
0.3.0), stats, utils, selectr, S4Vectors, R.utils,
SummarizedExperiment (>= 1.4.0), genefilter, readr,
RColorBrewer, doParallel, GenomeInfoDb, GenomicFeatures,
parallel, tools, tidyr, sva, limma, purrr, xml2, httr (>=
1.2.1), purrrogress, ggrepel (>= 0.6.3)
shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly,
readr, maftools, stringr (>= 1.1.0), SummarizedExperiment,
ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>=
2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel,
TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker,
sesame, shinyBS (>= 0.61)
AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures,
GenomicRanges, GenomicDataCommons, IRanges, methods,
MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest,
S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
methods, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils
arules, fields, GenomicRanges, graphics, stringr, methods,
stats, gplots
GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices,
dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges, methods
methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0),
graphics, Hmisc, limma, methods, magrittr, proxy, stats,
tibble, tidyr, vegan, viridis, utils
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma,
GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid,
stats, methods
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth,
graphics, grDevices, stats
Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment,
gRbase, limma, corpcor
methods, utils, stats, assertthat, ggplot2
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.2.10),
MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.11.4)
biobroom, broom, data.table, doParallel, foreach,
futile.logger, ggplot2, grDevices, gridExtra, grid, knitr,
limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr,
purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines,
stats, stringr, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz,
Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools,
IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix,
Rgraphviz, InteractionSet, graph, utils
mgcv, edgeR, SingleCellExperiment, SummarizedExperiment,
slingshot, magrittr, RColorBrewer, clusterExperiment,
BiocParallel, pbapply, ggplot2, princurve, methods, S4Vectors
biomaRt, data.table, doSNOW, foreach, ggplot2, graphics,
grDevices, igraph, limma, parallel, progress, RedeR, snow,
stats, tidyr, topGO
BiocGenerics, caret, chipseq, e1071, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2,
Rsamtools, rtracklayer, S4Vectors, stats, utils
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
ggseqlogo (>= 0.1), gridExtra (>= 2.3), methods, parallel, Rcpp
(>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8),
utils
BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots
ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,
tidytree (>= 0.2.6), utils
methods, utils, ape, dplyr, SummarizedExperiment
RSQLite, RMySQL, lassopv, randomForest, flare, vbsr, xgboost,
BiocParallel, RPostgreSQL, methods, DBI, BSgenome,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38,
org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.6.1)
stringr, S4Vectors, methods, assertive, BiocGenerics, IRanges,
XVector, Biostrings, Modstrings, ggplot2, scales
Biostrings, BiocGenerics, stringr, xml2, S4Vectors, assertive,
methods, httr, IRanges, utils
methods, assertive, stringr, BiocGenerics, Biostrings,
Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb,
rtracklayer, BSgenome, Rsamtools
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, cgdsr, igraph, grid,
gridExtra, xtable, gtable, scales, R.matlab, grDevices,
graphics, stats, utils, methods
ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv,
mclust, gplots
AnnotationHub, BiocGenerics, BiocParallel, dplyr,
GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools,
IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer,
S4Vectors, SummarizedExperiment, tools, utils
AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges,
GGally, ggplot2, Gviz, limma, IRanges (>= 2.7.1), reshape2,
Rsamtools, S4Vectors (>= 0.11.11), SummarizedExperiment,
VariantAnnotation (>= 1.19.9)
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
SummarizedExperiment, tximport, jsonlite, S4Vectors,
GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb,
Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs,
utils, methods
methods, rjson, GenomicRanges, IRanges, BiocParallel,
GenomeInfoDb, S4Vectors, SummarizedExperiment, utils
AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings,
BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures,
GenomeInfoDb, GenomeInfoDbData, GenomicAlignments,
GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments,
Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles,
shinyjs, Sushi, yaml
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation
methods, stats, utils, MASS, ggplot2, ape, ggtree, ggseqlogo,
yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics,
processx, S4Vectors, rlang
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0),
oligoClasses (>= 1.31.1), foreach, matrixStats, data.table,
grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools,
stats, utils, BSgenome.Hsapiens.UCSC.hg18
MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines,
colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>=
1.1-10), doParallel, grDevices, graphics, utils, stats
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges
(>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6),
AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome
(>= 1.47.3), GenomicFeatures (>= 1.31.3)
tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray,
SeqVarTools, DelayedArray, Biostrings, IRanges
utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>=
2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings
(>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>=
1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>=
1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny,
shinythemes, shinyjs, DT, shinyTree
Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel,
GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7),
BiocParallel, GenomeInfoDb, BSgenome, Biobase
tools, GenomicRanges, VariantAnnotation (>= 1.29.3),
GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools
utils, grDevices, stats, methods, dplyr, purrr, tibble,
magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger
Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr,
RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment,
tidyr, utils
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, AnnotationForge, biomaRt,
dendextend, DiagrammeR, DT, dynamicTreeCut, GOSemSim, ggplot2,
GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods,
plotly, topGO, RColorBrewer, R.utils, scales, stats, UpSetR,
utils, webshot
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq, Biobase
Rcpp (>= 1.0.1), arm (>= 1.10-1), BiocFileCache, BiocParallel,
SingleCellExperiment, parallel, methods, stats
methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>=
2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>=
1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7),
seqinr, stringr, wmtsa
methods, affy, preprocessCore, GenomicRanges, waveslim,
IRanges
multtest, qvalue, stats, utils, BiocManager
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
limma, matrixStats, locfit, stats, graphics
pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr,
magrittr, roar
stats, utils, data.table, IRanges, VariantAnnotation,
seqminer, ggplot2, biomaRt, readxl, S4Vectors
mzR (>= 2.19.5), BiocGenerics, ProtGenerics (>= 1.17.2),
lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet
(>= 1.5.2), S4Vectors, robustbase, IRanges
BiocGenerics, genefilter, graphics, grDevices, gtools,
MergeMaid, methods, stats, utils, mvtnorm, RColorBrewer,
GeneMeta, siggenes
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb,
reshape2, gridExtra, corrplot, dendextend, GetoptLong,
circlize, gtrellis, PMCMR, ComplexHeatmap, KEGGREST, grDevices
biomaRt, downloader, edgeR, gplots, graphics, limma,
matrixStats, preprocessCore, readr, RColorBrewer, stats,
quantro
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Rcpp, RcppArmadillo, RcppProgress, BH, RcppParallel
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>=
1.3.3), RcppParallel
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.7.1), cytolib(>=
1.7.4), RcppParallel
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings
Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
Matrix, testthat, rmarkdown, knitr, BiocStyle, SuperLearner,
earth, gam, nnls, airway
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl,
rmarkdown
simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf,
genefilter, estrogen, annaffy, gcrma
testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
knitr, testthat, alpineData, rtracklayer, ensembldb,
BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
knitr, rmarkdown, ComplexHeatmap, circlize, testthat
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, usethis
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,
hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,
org.Hs.eg.db, reactome.db, AnnotationForge, graph,
EnsDb.Hsapiens.v75, BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens,
hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager
IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR,
Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData
BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2,
testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Ggallus.UCSC.galGal5.refGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene
knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi,
TBX20BamSubset, Rsamtools, ggplot2, testthat
DESeq2, airway, knitr, rmarkdown, testthat
MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy,
gcrma, hugene10sttranscriptcluster.db
RColorBrewer, crlmm, ff,
BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19,
lattice, latticeExtra, RUnit, BiocGenerics
knitr, rmarkdown, BiocStyle, testthat, ASICSdata
testthat, BiocStyle, lintr, knitr, rmarkdown
BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
MotifDb, trackViewer, testthat
Biobase, BiocStyle, devtools, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat,
zoo
testthat (>= 2.1.0), covr, knitr, rmarkdown, mtbls2
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, BiocStyle, knitr, beachmat, scran, scRNAseq
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, devtools
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
aCGH, affy, limma, snapCGH, beadarray, DNAcopy
testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF
testthat, BiocStyle, knitr, rmarkdown, pander
BiocGenerics, BiocStyle, minfiData, parallel,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
SummarizedExperiment
BiocStyle, rmarkdown, knitr, testthat (>= 0.10.0)
RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools
(>= 1.4.1), usethis, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,
Biostrings, Rsamtools, AnnotationDbi, oligoClasses, oligo,
affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit
testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy,
RcppHNSW
knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle,
ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>=
1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene,
Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat,
AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75
reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim,
testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot,
targetscan.Hs.eg.db, Hmisc, spelling
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,
BiocStyle, knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC,
pdftools, visNetwork, clipr, blastula, kableExtra
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, beachmat
annotate, BiocStyle, knitr, rmarkdown, testthat
cluster, parallel, GenomicFeatures, dynamicTreeCut,
Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, org.Hs.eg.db, ineq, covr
BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db,
knitr, omicade4, rmarkdown, testthat
BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit
knitr, markdown, base, rmarkdown, ggplot2
testthat, knitr, rmarkdown, BiocStyle, earth, glmnet,
randomForest, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1)
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat,
QDNAseq.hg19, QDNAseq.mm10
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
BiocStyle, knitcitations, knitr, rmarkdown, sessioninfo,
testthat (>= 2.1.0)
BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,
BSgenome.Scerevisiae.UCSC.sacCer1,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat
(>= 1.5.2), BatchJobs
testthat, RUnit, doParallel, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat, BiocStyle, TENxBUSData,
DropletUtils, ggplot2, TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm9.knownGene
BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE,
BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl,
gplots
BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical
BiocStyle, knitr, rmarkdown, testthat, diffcyt
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGG.db, karyoploteR, geneplotter, limma, lattice,
RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter
crossmeta, knitr, rmarkdown, testthat, lydata
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix,
biomaRt, covr, M3DExampleData, BiocManager, BiocStyle
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
BiocStyle, knitr, rmarkdown, testthat, limma
data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics,
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db,
Biobase, tools
ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap,
BiocManager
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>=
1.16.1), ChemmineDrugs, png,rmarkdown, BiocManager
knitr, rmarkdown, Matrix, testthat, vdiffr
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
Rsamtools, GenomicInteractions, GenomicRanges, IRanges,
AnnotationHub
testthat, roxygen2, devtools, knitr, lintr
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle,
gridExtra (>= 2.2), testthat
reactome.db, BSgenome.Ecoli.NCBI.20080805,
BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr,
rmarkdown, testthat, trackViewer, motifStack, OrganismDbi
clusterProfiler, ggimage, ggplotify, ggupset, ReactomePA,
org.Hs.eg.db, knitr, rmarkdown, testthat, tibble
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3),
GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3),
testthat
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>=
1.36.6), testthat, vdiffr (>= 0.2.3), covr
knitr, testthat, ReactomePA, RUnit, BiocGenerics,
AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db,
biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods,
Biostrings,Homo.sapiens
testthat, knitr, roxygen2, rmarkdown, citr, devtools,
gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0),
gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu,
parathyroidSE, knitr, htmltools, gtable, scales, e1071,
rmarkdown, IRanges, randomForest, robustbase, glmnet, class
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.1.4)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr,
CluMSIDdata, metaMS, metaMSdata, xcms
BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran,
igraph
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db,
prettydoc, ReactomePA, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Ggallus.UCSC.galGal3
minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, Gviz, MultiAssayExperiment, TCGAutils,
curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
genefilter, mvtnorm, testthat (>= 0.3), data.tree,
dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap,
clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots,
hu6800.db
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2
BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>=
2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0)
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg,
tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2,
glue, GenomicRanges
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, minfiData, RCurl
BiocStyle, knitr, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
glpkAPI, testthat, knitr, rmarkdown, digest, R.cache,
ggplot2, plyr, igraph, methods, latex2exp,
rBayesianOptimization
knitr, kableExtra, BiocStyle, Biobase, roxygen2,
RColorBrewer, devtools, xtable
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown,
rtracklayer, sangerseqR, testthat, VariantAnnotation
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
RUnit
rmarkdown, testthat, knitr, shiny, shinydashboard,
shinyWidgets, shinycssloaders, DT, ggthemes, ggplot2, pheatmap,
RColorBrewer, tibble, ggalluvial
knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle,
flowStats
testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel
XML, BiocStyle, knitr, rmarkdown, testthat
EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust,
minqa, SummarizedExperiment, Biobase, knitr, rmarkdown,
BiocStyle, edgeR
mgcv, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
HDF5Array, genefilter, SummarizedExperiment, airway, pryr,
DelayedMatrixStats, knitr, BiocStyle, RUnit
testthat, knitr, rmarkdown, SeqArray, GDSArray
testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark,
profmem
Rtsne, testthat, knitr, rmarkdown, BiocStyle
BiocStyle (>= 2.5.19), biovizBase, sessioninfo, derfinderData
(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>=
1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>=
0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene
sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6),
BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat
biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData
(>= 0.99.0), sessioninfo, knitcitations (>= 1.0.1), knitr (>=
1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR,
rmarkdown (>= 0.3.3), testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq,
RUVSeq, RColorBrewer, statmod
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW,
apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,
airway, pasilla (>= 0.2.10)
nbconvertR (>= 1.3.2), igraph, testthat, FNN, tidyr
knitr, rmarkdown, testthat, BiocStyle, IHW
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2
lattice, parallel, MASS, RColorBrewer, xtable
knitr, RUnit, BiocGenerics,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC
(>= 1.15.0), RUnit, simulatorZ, proxy
prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat
covr, testthat, knitr, rmarkdown, BiocStyle
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
testthat, beachmat, knitr, BiocStyle, rmarkdown
limma, convert, GEOquery, dyebiasexamples, methods
BiocStyle (>= 2.12.0), BSgenome (>= 1.52.0),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr,
rmarkdown, RUnit (>= 0.4.32)
BiocStyle, digest, knitr, rmarkdown, shiny
ecoliLeucine, ecolicdf, graph, multtest, affy
BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR,
KernSmooth, testthat
AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines
igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust,
MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db,
org.Hs.eg.db
DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer,
hgu133plus2cdf, hgu133plus2probe
BiocStyle, knitr, testthat, data.table, DT,
GenomicInteractions, webshot, R.utils, covr
RUnit,BiocGenerics,knitr, curl, httr, shiny, shinythemes, DT
RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway,
gridExtra, magrittr
testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
ALL, BiocStyle, ReportingTools, airway, hgu95av2.db, knitr
clusterProfiler, dplyr, ggupset, knitr, org.Hs.eg.db,
prettydoc, tibble
BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
1.20.0), magrittr, AnnotationHub
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db
testthat, roxygen2, knitr, Biobase, SummarizedExperiment,
antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle
testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors,
IRanges, SummarizedExperiment, antiProfilesData,
hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny,
minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr,
AnnotationHub
testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus,
TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown,
BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer,
utils, RMySQL, DBI
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg,
testthat, webshot
ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment
BiocStyle, knitr, rmarkdown, kableExtra, magrittr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
caret, mlbench, SingleCellExperiment, knitr, rmarkdown,
testthat, BiocManager
testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData,
scater, gridExtra, scran, Seurat, knitr
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db,
reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr,
rmarkdown, AnnotationDbi, RGtk2, BiocManager
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery
BiocStyle, testthat, knitr, rmarkdown, reutils
testthat, knitr, rmarkdown, macrophage, tximeta,
org.Hs.eg.db, samr, DESeq2, apeglm
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
testthat, knitr, rmarkdown, BiocStyle, flowVS, vulcan,
DepecheR
BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat,
BiocStyle
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments,
stats
testthat, flowWorkspaceData, knitr, ggcyto, parallel, CytoML,
openCyto
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene
pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db,
GSEABase, Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma
org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db,
org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db,
org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db,
org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc,
ggplot2, kableExtra, profvis, reshape2
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa
affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db,
org.Hs.eg.db, org.Mm.eg.db, RUnit
edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db,
org.Hs.eg.db, RUnit, BiocGenerics
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, crayon, RUnit, knitr, BiocGenerics
RUnit, rentrez, knitr, rmarkdown, BiocStyle
assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat
GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi,
org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat
class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla,
RColorBrewer, BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival
RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny,
STRINGdb, BiocStyle, magick
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
CompQuadForm, poibin, SPAtest, survey, testthat, BiocStyle,
knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db,
org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods
BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter
(>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown
BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown
GenomicRanges, Rsamtools, GenomicAlignments, BSgenome,
GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
ShortRead, rtracklayer, BSgenome, GenomicFeatures,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,
DESeq2, edgeR, RUnit, BiocStyle
BiocStyle, knitr, rmarkdown, DT, testthat, listviewer,
ggplot2, GenomicAlignments, Rsamtools
RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome,
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7),
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6),
SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit,
BiocStyle, knitr
BiocStyle, RUnit, genefilter, deepSNV,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
BiocStyle
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5,
SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation,
TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer
testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats,
BSgenome, Biostrings
testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape,
xtable
BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL,
roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg38
knitr, rmarkdown, BiocGenerics, testthat, covr
vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat,
EnsDb.Hsapiens.v75, tinytex
testthat, flowWorkspaceData, knitr, rmarkdown, flowStats,
openCyto, flowViz, ggridges, vdiffr
GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc,
rmarkdown, scales, stats, testthat, tibble
roxygen2, knitr, rmarkdown, testthat, BiocStyle
BiocStyle, IRanges, GenomicRanges, SummarizedExperiment,
DESeq2, limma, testthat, knitr, rmarkdown, pryr
testthat, knitr, rmarkdown, survival, survcomp, pROC,
VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, testthat
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics
geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools,
Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack
geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio,
BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock
SparseM (>= 0.36), XML, RBGL, RUnit, cluster
a4Preproc, ALL, BiocStyle, clipper, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
SummarizedExperiment, knitr, plotly, RANKS, WGCNA
limma, RColorBrewer, genefilter, edgeR, snow, parallel,
GSVAdata
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown,
testthat
DO.db, DT, knitr, RBGL, RUnit, snpStats, Gviz,
VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio,
ggplot2, DelayedArray
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
VariantAnnotation
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0)
h5vcData, SummarizedExperiment (>= 1.15.1), GenomicRanges,
ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures,
BiocStyle
parallel, knitr, gdsfmt (>= 1.2.2), SNPRelate (>= 1.1.6),
ggplot2, reshape2
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat
KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow
knitr, BiocStyle, beeswarm, tximportData, DT, tximport,
dplyr, magrittr, BiocFileCache, testthat
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, Rsubread (>= 1.29.0), testthat
testthat, BiocStyle, airway, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, gridExtra, ggrepel
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
RUnit, hgu95av2.db, knitr, GenomicRanges,
SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer,
metagenomeSeq, gplots, vegan, Biobase
BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db,
org.Hs.eg.db
RDAVIDWebService, gProfileR, topGO, KEGGprofile,
org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater,
DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis,
org.Mm.eg.db, htmltools
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap,
BiocStyle, testthat
knitr, png, limma, grid, DT, randomForest, digest, testthat
BiocStyle, knitr, testthat, magrittr,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db,
pasillaBamSubset
Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db,
org.Hs.eg.db, hgu133plus2.db, SPIA
affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db,
gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines,
statmod (>= 1.2.2), vsn
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments,
testthat
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr,
spelling, testthat
knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable,
gridExtra, RColorBrewer, seqLogo, ggseqlogo
parallel, testthat, knitr, BiocStyle, rmarkdown
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
ROCR, knitr, M3DExampleData, scater, SingleCellExperiment,
monocle, Seurat, Biobase
knitr, rmarkdown, BSgenome, Biostrings, NMF, mclust
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
biomaRt (>= 2.34.1), httr (>= 1.2.1), IRanges (>= 2.8.2),
knitr, testthat, tidyverse, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, AnnotationHub
knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(>
6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer,
BiocStyle, scater, DelayedArray, Matrix, HDF5Array
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, knitr, testthat
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k,
knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit,
BiocGenerics
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle,
rmarkdown, similaRpeak
BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay
BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager,
BSgenome, RSQLite
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, curatedMetagenomicData
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
knitr, rmarkdown, DSS, bsseq, plotly,
BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38,
MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings,
RColorBrewer, GenomicRanges, GenomeInfoDb, IRanges, testthat
(>= 2.1.0)
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
RUnit
knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr,
ggplot2
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit,
methInheritSim
BiocStyle, doParallel, testthat, knitr, rmarkdown
lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
parallel, rtracklayer, Biostrings, methyAnalysis,
TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth,
nnet, gam, arm, snow, parallel, BatchJobs, minfiData,
methyvimData
BiocGenerics, BiocStyle, Cairo, knitcitations, knitr,
rmarkdown, testthat
breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG,
breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ,
MIGSAdata
knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind,
affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1
biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX
IlluminaHumanMethylation450kmanifest (>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>=
1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools
human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit
seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>=
1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell,
IRanges, GenomicRanges (>= 1.8.3), BSgenome,
beadarrayExampleData
BiocGenerics, RUnit, knitr, rtracklayer, utils
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
minfiData, BiocStyle, knitr, rmarkdown, edgeR,
tweeDEseqCountData
BiocStyle, knitr, rmarkdown, testthat, rgl
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party
testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0)
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma,
mouse4302.db, reactome.db
knitr, testthat, BiocStyle, VennDiagram, pamr
testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle,
MMAPPR2data
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
GOstats, graph, Category, org.Mm.eg.db, microRNA,
targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid,
class, cluster, multtest, RColorBrewer, latticeExtra
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png
BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608,
SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown,
BSgenome.Drerio.UCSC.danRer7, BiocStyle
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr,
httr, htmltools
testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr,
SummarizedExperiment
BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData,
CAMERA, RPostgres, RMySQL
MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2,
pkgdown, knitr, rsvg
BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array,
RaggedExperiment, UpSetR, survival, survminer
knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase,
GEOquery
brgedata, minfi, minfiData, knitr, rmarkdown, testthat,
omicade4, iClusterPlus, GEOquery, MultiAssayExperiment,
BiocStyle, RaggedExperiment
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
BiocStyle, cowplot, ExperimentHub, knitr, RColorBrewer,
rmarkdown, testthat, UpSetR
BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5
(>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle
(>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>=
1.32.2), testthat
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat, BiocManager
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit
Starr, BiocStyle, knitr, rmarkdown, testthat
BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2,
pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma,
RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl
hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6),
RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm
BiocStyle, knitr, rmarkdown, snpStats, brgedata
knitr, rmarkdown, testthat, devtools, BiocManager
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
tidyr, dnet, gprofiler2, BiocStyle, testthat
BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots,
GenomicRanges, kableExtra
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle
flowWorkspaceData, knitr, testthat, utils, tools, parallel,
ggcyto, CytoML
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
testthat, rmarkdown, knitr, BiocStyle, BSgenome,
BSgenome.Hsapiens.UCSC.hg19
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat,
knitr, rmarkdown, BiocStyle, ggplot2
Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19,
AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit,
RMariaDB
testthat, knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB,
AnnotationDbi, beeswarm, covr
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
BiocStyle, knitr, rmarkdown, testthat, digest
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gQTLBase, gQTLstats, geuvStore2, gwascat, BiocStyle
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt,
estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW,
parallel, org.Hs.eg.db
testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr,
rmarkdown, BiocStyle, EnsDb.Hsapiens.v86 (>= 2.0.0)
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db,
hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db,
pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9,
pcaGoPromoter.Rn.rn4, serumStimulation, parallel
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
biomaRt, ggplotify, beachmat
testthat, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
testthat, lintr, knitr, rmarkdown, BiocStyle
RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics,
BiocStyle, knitr, R.utils
GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma
testthat, BiocStyle, knitr, rmarkdown, data.table
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet,
dplyr
foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview,
tidyr, dplyr
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>=
2.30.0), knitr, BiocStyle, AnnotationDbi, energy
knitr, htmltools, BiocStyle, rmarkdown, testthat
knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0),
HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19,
pasillaBamSubset, covr, ggplot2
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
BiocStyle, knitr, rmarkdown, colr, metap, repmis
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
BiocStyle, knitr, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra,
roxygen2, testthat (>= 2.1.0), spelling
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown
BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools,
ggplot2
airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr,
readr, readxl
BiocStyle, gridExtra, grid, testthat, devtools, knitr,
rmarkdown, ComplexHeatmap, viridis, ggplot2
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2,
synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3),
dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown
RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
testthat (>= 2.1.0), knitr, rmarkdown, gridExtra
pumadata, affydata, snow, limma, ROCR,annotate
BiocParallel, BiocStyle, PSCBS,
TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr,
optparse, org.Hs.eg.db, rmarkdown, testthat
MotifDb, BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel,
PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background,
BiocStyle, knitr
affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX,
RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown, BiocManager
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
Gviz, BiocStyle, knitr, rmarkdown, covr, testthat
QUBICdata, qgraph, fields, knitr, rmarkdown
BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene,
biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny,
ChIPpeakAnno
BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Rnorvegicus.UCSC.rn5.masked
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
h5vcData, testthat, knitr, optparse,
BSgenome.Hsapiens.UCSC.hg19
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL,
igraph
limma, biomaRt, RUnit, BiocGenerics, BiocStyle
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10,
BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db,
org.Dm.eg.db, testthat, covr
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW,
parallel
Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp,
rmarkdown, testthat, visNetwork, arrow
RUnit, BiocStyle, RefNet, knitr, rmarkdown
testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase,
devtools
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc,
testthat
AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2,
sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures,
knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR,
regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>=
2.1.0)
grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown,
zoo, RUnit, BiocManager, BSgenome, RSQLite, RMySQL
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio (>= 1.13.13),
ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, minfiDataEPIC
RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla,
org.Sc.sgd.db
knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db,
BiocStyle, restfulSEData
mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown
RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve
RUnit, BiocStyle, BiocGenerics, xtable, sna
testthat (>= 0.3), knitr, circlize (>= 0.4.8), rmarkdown
boot, tools, BiocGenerics, knitr, xtable
bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark,
dplyr, ggplot2
knitr, testthat, BiocStyle, DT, reticulate
knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, RUnit,
enviPat
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
Biostrings, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data,
RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer,
keras
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
RNAmodR.Data
Category, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel,
ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva,
wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD,
IlluminaHumanMethylation450kanno.ilmn12.hg19, scales,
missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit,
MethylSeekR
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat,
lubridate, DT, rmarkdown,
BiocGenerics, BiocStyle, knitr, multtest, omicade4,
rmarkdown, testthat
org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db,
org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db,
hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI
MSnbase, Biostrings, BiocStyle, testthat, knitr
GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr
BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit,
BiocGenerics
BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1),
genefilter, limma, org.Hs.eg.db, hgu133plus2.db,
GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,
knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked,
org.Hs.eg.db, org.Mm.eg.db, ggplot2
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
parallel, crayon, RUnit, knitr, BiocGenerics, SNPRelate
RUnit, BiocGenerics, knitr, knitcitations, formatR,
org.Sc.sgd.db, BioNet, DLBCL, msm
BiocStyle, BiocFileCache, biomaRt, beachmat, cowplot,
destiny, knitr, scRNAseq, robustbase, rmarkdown, Rtsne, uwot,
testthat, pheatmap, Biobase, limma, DropletUtils
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot
testthat, knitr, rmarkdown, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown,
RColorBrewer, ReactomePA, clusterProfiler, cowplot,
org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne,
BiocParallel, e1071, WGCNA, devtools, DOSE
ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr,
TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
scater, testthat, badger
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase,
BiocGenerics, ggplot2, ggthemes
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork,
doParallel, BatchJobs
testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle,
Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment
testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq,
dynamicTreeCut, DESeq2, monocle, Biobase, aroma.light, pheatmap
BiocStyle, knitr, rmarkdown, Rsubread, testthat
testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db,
MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, Rsamtools, VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
testthat, BiocStyle, knitr, rmarkdown, covr
BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr,
cowplot, knitr, rmarkdown, testthat
scales, knitr, rmarkdown, testthat, minfi,
SummarizedExperiment, FlowSorted.CordBloodNorway.450k,
FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
testthat, parallel, knitr, rmarkdown, BiocStyle
shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
BiocStyle, optparse, testthat, knitr, rmarkdown
org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db
IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr,
rmarkdown
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph
RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc
BiocStyle, knitr, biomaRt, stringr, monocle
testthat, BiocStyle, knitr, rmarkdown, scRNAseq, Rtsne,
Matrix
testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch,
rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable,
spelling, GSEABase
testthat, knitr, rmarkdown, BiocStyle, beachmat,
SingleCellExperiment, scater, scRNAseq, scran, BiocGenerics,
ggplot2, pheatmap, grDevices, viridis, AnnotationHub,
AnnotationDbi
BiocGenerics, BiocStyle, clusterExperiment, destiny, gam,
knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat,
covr
GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2,
Rtsne, Biobase, BiocStyle
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress,
pscl, testthat, rmarkdown, scDD, scran, mfa, phenopath, BASiCS
(>= 1.7.10), zinbwave, SparseDC, BiocManager, spelling, igraph,
DropletUtils
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel,
gridExtra, digest, doParallel, bigmemory
RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
qgraph, png, grid
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
testthat, BiocStyle, knitr, rmarkdown,
gWidgets2,gWidgets2RGtk2,RGtk2
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat,
roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize,
tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat,
DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter,
scater, rnaseqcomp, biomaRt
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit,
testthat
Hmisc, CPE, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt,
BiocParallel, BiocManager
testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS,
covr
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame,
pathview, clusterProfiler, ComplexHeatmap, circlize,
ConsensusClusterPlus, igraph, TCGAbiolinksGUI.data, supraHex
testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2,
BiocStyle, animation, pander
BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap,
devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19,
impute, knitr, magrittr, mirbase.db, org.Hs.eg.db,
RColorBrewer, readr, RTCGAToolbox (>= 2.7.5), rtracklayer,
R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2,
GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, data.table, testthat, AnnotationDbi, AnnotationFilter,
Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges,
Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75,
BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb,
SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb,
motifStack, RColorBrewer
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap,
GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db,
MASS, RColorBrewer, rmarkdown, UpSetR,
knitr, aroma.light, affxparser, RUnit, BiocGenerics
GenomicFeatures, shiny, BiocManager, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats,
Matrix
EBImage, knitr, rmarkdown, testthat, tofsimsData,
BiocParallel, RColorBrewer
BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR,
plotrix, breastCancerVDX, EnrichmentBrowser
limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr,
rmarkdown, reshape2, tidyr, readr, org.At.tair.db,
AnnotationDbi
topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle,
xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr,
htmltools
knitr, rmarkdown, cowplot, dplyr, tidyr, testthat
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
Biostrings, ggplot2, ggtree, igraph, knitr, phangorn,
prettydoc, testthat, tidyr, vroom
ggtree, BiocStyle, knitr, rmarkdown, testthat
RUnit, plyr, knitr, BiocGenerics, rmarkdown,
BSgenome.Scerevisiae.UCSC.sacCer3
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer
BiocStyle, knitr, rmarkdown, testthat, ggplot2,
BSgenome.Scerevisiae.UCSC.sacCer3
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways
EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT
(>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>=
1.12), rmarkdown, testthat, covr, pander
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
DESeq2, edgeR, limma, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, csaw, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, fishpond
knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny,
biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb,
ontoProc, rjson, graph, TFutils (>= 1.5.4)
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, knitr, rmarkdown, BiocGenerics, RUnit
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics,
r2glmm, readr
RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle
RUnit, BiocStyle, org.Hs.eg.db,
BSgenome.Hsapiens.1000genomes.hs37d5,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19,
PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>=
1.21.3)
SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData,
pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22
knitr, rmarkdown, biomaRt, GenomicFeatures, testthat,
ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi,
AnnotationFilter
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
knitr, DESeq, rmarkdown, BiocStyle, testthat
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, rgl, microbenchmark, testthat, pander,
magrittr, MALDIquant, pheatmap
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr,
rmarkdown
MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk
knitr, limma, edgeR, GEOquery, stringr, printr
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat
Rsubread, BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene
parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno,
org.Dm.eg.db, caTools, plotly
rGADEM, seqLogo, genoPlotR, parallel, VennDiagram,
RColorBrewer, vcd, MotifDb, snowfall
iplots, reshape, ggplot2, cairoDevice, OTUbase
doMC, doMPI, doSNOW, doParallel, doRedis
parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
doSNOW, VanillaICE (>= 1.21.24), RColorBrewer